fail to open fasta index

[James Doonan]

Hi all,

I'm stumped on an error, which seems to indicate that Emirge cant open the fasta index file;

emirge.py . -1 forward.fastq -2 reverse.fastq -f SSURef_111_candidate_db_fixed.fasta -b SSURef_111_candidate_dbindex. --mapping test -l 100 -i 110 -s 30 --phred33
If you use EMIRGE in your work, please cite these manuscripts, as appropriate.

imported _emirge C functions from: /usr/local/lib/python2.7/dist-packages/_emirge.so
Command:
/usr/local/bin/emirge.py . -1 forward.fastq -2 reverse.fastq -f SSURef_111_candidate_db_fixed.fasta -b SSURef_111_candidate_dbindex. --mapping test -l 100 -i 110 -s 30 --phred33

EMIRGE started at Sun May 17 19:04:17 2015
Beginning initialization at Sun May 17 19:04:17 2015...
Reading bam file /home/james/Documents/EMIRGE/test at Sun May 17 19:04:17 2015...
DONE Reading bam file /home/james/Documents/EMIRGE/test at Sun May 17 19:04:25 2015 [0:00:08.102563]...
DONE with initialization at Sun May 17 19:04:25 2015...
Starting iteration 0 at Sun May 17 19:04:25 2015...
Reading bam file /home/james/Documents/EMIRGE/test at Sun May 17 19:04:25 2015...
DONE Reading bam file /home/james/Documents/EMIRGE/test at Sun May 17 19:04:30 2015 [0:00:04.764734]...
Calculating likelihood (66, 271902) for iteration 0 at Sun May 17 19:04:30 2015...
    Calculating Pr(N=n) for iteration 0 at Sun May 17 19:04:30 2015...
    DONE calculating Pr(N=n) for iteration 0 at Sun May 17 19:04:32 2015 [0:00:01.941272]...
DONE Calculating likelihood for iteration 0 at Sun May 17 19:04:34 2015 [0:00:03.939788]...
Calculating posteriors for iteration 0 at Sun May 17 19:04:34 2015...
DONE Calculating posteriors for iteration 0 at Sun May 17 19:04:34 2015 [0.045 seconds]...
Writing consensus for iteration 0 at Sun May 17 19:04:34 2015...
    snp_minor_prob_thresh = 0.100
    snp_percentage_thresh = 0.040
splitting sequence 0 (GU366042.1.1200) to 66 (GU366042.1.1200_m01)...
    Split out 1 new minor strain sequences.
    Average time for split sequence: [0.233058 seconds]
    Average time for posterior update: [0.231215 seconds]
    Average time for non-split sequences: [0.000004 seconds]
    Culled 65 sequences
DONE Writing consensus for iteration 0 at Sun May 17 19:04:35 2015 [0:00:00.432150]...
Clustering sequences for iteration 0 at Sun May 17 19:04:35 2015...
    cluster threshold = 0.970
[fai_load] build FASTA index.
[fai_load] build FASTA index.
usearch command was:
usearch -search_global /home/james/Documents/EMIRGE/iter.00/iter.00.cons.fasta.tmp.fasta --db /home/james/Documents/EMIRGE/iter.00/iter.00.cons.fasta.tmp.fasta --id 0.800 -quicksort -query_cov 0.5 -target_cov 0.5 -strand plus --userout /home/james/Documents/EMIRGE/iter.00/iter.00.cons.fasta.tmp.fasta.us.txt --userfields query+target+id+caln+qlo+qhi+tlo+thi -threads 1 -fulldp
usearch v8.0.1517_i86linux32, 4.0Gb RAM (11.5Gb total), 1 cores
(C) Copyright 2013-15 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

Licensed to: bsp...@bangor.ac.uk

00:00  36Mb    0.1% Reading /home/james/Documents/EMIRGE/iter.00/iter.00.cons.fa00:00  40Mb  100.0% Reading /home/james/Documents/EMIRGE/iter.00/iter.00.cons.fasta.tmp.fasta
00:00 6.1Mb    0.1% Masking                                                     00:00 6.1Mb  100.0% Masking
00:00  42Mb  100.0% Searching iter.00.cons.fasta.tmp.fasta, 100.0% matched

WARNING: Option -quicksort ignored

Writing new fasta file for iteration 0 at Sun May 17 19:04:35 2015...
    removed 0 sequences after merging
    sequences remaining for iteration 00: 2
DONE Clustering sequences for iteration 0 at Sun May 17 19:04:35 2015 [0:00:00.130133]...
Writing priors and probN to disk for iteration 0 at Sun May 17 19:04:35 2015...
DONE Writing priors and probN to disk for iteration 0 at Sun May 17 19:04:35 2015...
Starting read mapping for iteration 0 at Sun May 17 19:04:35 2015...
    bowtie-build command:
    bowtie-build -o 3 /home/james/Documents/EMIRGE/iter.00/iter.00.cons.fasta /home/james/Documents/EMIRGE/iter.00/bowtie.index.iter.00 > /home/james/Documents/EMIRGE/iter.00/bowtie.iter.00.log 2>&1
    bowtie command:
    cat  /home/james/Documents/EMIRGE/forward.fastq |  bowtie --phred33-quals -t -p 1  -n 3 -l 20 -e 300  --best --strata --all --sam --chunkmbs 128 --minins 100 --maxins 200 /home/james/Documents/EMIRGE/iter.00/bowtie.index.iter.00 -1 - -2 /home/james/Documents/EMIRGE/reverse.fastq | samtools view -b -S -F 0x0004 - > /home/james/Documents/EMIRGE/iter.00/bowtie.iter.00.PE.bam 2> /home/james/Documents/EMIRGE/iter.00/bowtie.iter.00.log
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Seeded quality full-index search: 00:00:17
# reads processed: 135951
# reads with at least one reported alignment: 2 (0.00%)
# reads that failed to align: 135949 (100.00%)
Reported 4 paired-end alignments to 1 output stream(s)
Time searching: 00:00:17
Overall time: 00:00:17
    Finished Bowtie for iteration 00 at Sun May 17 19:04:52 2015:
DONE with read mapping for iteration 0 at Sun May 17 19:04:52 2015...
Finished iteration 0 at Sun May 17 19:04:52 2015...
Total time for iteration 0: 0:00:26.137206
Starting iteration 1 at Sun May 17 19:04:52 2015...
Reading bam file /home/james/Documents/EMIRGE/iter.00/bowtie.iter.00.PE.bam at Sun May 17 19:04:52 2015...
[fai_load] build FASTA index.
DONE Reading bam file /home/james/Documents/EMIRGE/iter.00/bowtie.iter.00.PE.bam at Sun May 17 19:04:52 2015 [0:00:00.195924]...
Calculating likelihood (67, 271902) for iteration 1 at Sun May 17 19:04:52 2015...
    Calculating Pr(N=n) for iteration 1 at Sun May 17 19:04:52 2015...
    DONE calculating Pr(N=n) for iteration 1 at Sun May 17 19:04:52 2015 [0:00:00.002210]...
DONE Calculating likelihood for iteration 1 at Sun May 17 19:04:52 2015 [0:00:00.002647]...
Calculating posteriors for iteration 1 at Sun May 17 19:04:52 2015...
DONE Calculating posteriors for iteration 1 at Sun May 17 19:04:52 2015 [0.008 seconds]...
Writing consensus for iteration 1 at Sun May 17 19:04:52 2015...
    snp_minor_prob_thresh = 0.100
    snp_percentage_thresh = 0.040
    Split out 0 new minor strain sequences.
    Average time for non-split sequences: [0.000000 seconds]
    Culled 2 sequences
DONE Writing consensus for iteration 1 at Sun May 17 19:04:52 2015 [0:00:00.005879]...
Clustering sequences for iteration 1 at Sun May 17 19:04:52 2015...
    cluster threshold = 0.970
[fai_load] build FASTA index.
[fai_load] fail to open FASTA index.
Traceback (most recent call last):
  File "/usr/local/bin/emirge.py", line 1697, in <module>
    main()
  File "/usr/local/bin/emirge.py", line 1688, in main
    do_iterations(em, max_iter = options.iterations, save_every = options.save_every)
  File "/usr/local/bin/emirge.py", line 1444, in do_iterations
    os.path.join(subdir, "iter.%02d.cons.fasta"%(em.iteration_i)))
  File "/usr/local/bin/emirge.py", line 500, in do_iteration
    self.cluster_sequences(consensus_filename)  # merges sequences that have evolved to be the same (USEARCH)
  File "/usr/local/bin/emirge.py", line 807, in cluster_sequences
    return self.cluster_sequences2(fastafilename)
  File "/usr/local/bin/emirge.py", line 829, in cluster_sequences2
    num_seqs = self.write_consensus_with_mask(fastafilename, tmp_fastafilename, mask="soft")
  File "/usr/local/bin/emirge.py", line 769, in write_consensus_with_mask
    reference_fastafile = pysam.Fastafile(reference_fastafilename)
  File "cfaidx.pyx", line 81, in pysam.cfaidx.FastaFile.__cinit__ (pysam/cfaidx.c:1701)
  File "cfaidx.pyx", line 105, in pysam.cfaidx.FastaFile._open (pysam/cfaidx.c:2272)
IOError: could not open file `/home/james/Documents/EMIRGE/iter.01/iter.01.cons.fasta`

Thanks,

James

[James Doonan]

I managed to get an error free output but only by removing all the --phred flags when passing to bowtie. I guess this would mean that my output file is less accurate?

[Chris Miller]

James,

In the current version of EMIRGE, you only have two options:

-- use 64-based quality score encoding (default)

-- use 33-based quality score encoding (by passing --phred33)

The second option (33-based) has been standard with Illumina output for a while now, and should be what most people choose (an in-development version of EMIRGE will figure this out on its own).

I notice this in your output for iter 00:

# reads processed: 135951
# reads with at least one reported alignment: 2 (0.00%)
# reads that failed to align: 135949 (100.00%)

...

Culled 2 sequences

That is, you have no sequences that have any reads mapping to them, so EMIRGE tosses all the candidates and you get an error because the fasta file has nothing in it.

What is your input?  You don't have very many reads if this is a metagenomic library.  Where did the initial mapping file you are using come from?

Chris

[James Doonan]

Hi Chris,

I was using small test files. So I guess this was the reason that there wasn't any mapping. I tried my actual files which are much larger and the program ran but stopped with this error when moving on to iteration 4;

Writing new fasta file for iteration 4 at Thu May 28 06:09:00 2015...
        removed 119 sequences after merging
        sequences remaining for iteration 04: 1726
DONE Clustering sequences for iteration 4 at Thu May 28 06:09:00 2015 [0:00:58.244717]...
Writing priors and probN to disk for iteration 4 at Thu May 28 06:09:00 2015...
DONE Writing priors and probN to disk for iteration 4 at Thu May 28 06:09:05 2015...
Starting read mapping for iteration 4 at Thu May 28 06:09:05 2015...
        bowtie-build command:
        bowtie-build -o 3 /home/james.doonan/EMIRGE/1/iter.04/iter.04.cons.fasta /home/james.doonan/EMIRGE/1/iter.04/bowtie.index.iter.04 > /home/james.doonan/EMIRGE/1/iter.04/bowtie.iter.04.log 2>&1
        bowtie command:
        cat  /home/james.doonan/RAY_combined_fastq_files/1_300bp_ACTTGA_L006_R1_001.fastq |  bowtie -t -p 1  -n 3 -l 20 -e 300  --best --strata --all --sam --chunkmbs 128 --minins 100 --maxins 270 /home/james.doonan/EMIRGE/1/iter.04/bowtie.index.iter.04 -1 - -2 /home/james.doonan/RAY_combined_fastq_files/1_300bp_ACTTGA_L006_R2_001.fastq | samtools view -b -S -F 0x0004 - > /home/james.doonan/EMIRGE/1/iter.04/bowtie.iter.04.PE.bam 2> /home/james.doonan/EMIRGE/1/iter.04/bowtie.iter.04.log

Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00

User defined signal 2

I tried to resume the job but this failed.

This is through my university HPC cluster.

Thanks,

James

On Sunday, May 17, 2015 at 7:12:08 PM UTC+1, James Doonan wrote:

[Chris Miller]

James,

Perhaps your queue has a maximum job runtime limit.  The cluster may have kicked your job out for taking too long.

Check the log, ask your administrator if there is a limit, and see if the two are comparable.  If this isn't the case, please attach or send via email the full log file.

Chris

[xulin...@gmail.com]

Hi Chris,

I met the same error as James. Here is the error report: I don't know what to do, I'm wondering can you help me? Thank you very much.

    ...merging 2546|GU362968.1.1396 into 742|GX182404.8.1529 (99.41% ID over 677 columns) in 0.001 seconds
    ...merging 2549|DQ646535.1.1789 into 796|JN397367.1.1797 (97.37% ID over 1331 columns) in 0.003 seconds
    ...merging 2551|EU471186.1.1218 into 479|FR877557.4039313.4040854 (100.00% ID over 647 columns) in 0.010 seconds
    ...merging 3396|HQ236044.1.1521 into 2555|FJ268976.1.1516 (99.90% ID over 992 columns) in 0.001 seconds
    ...merging 2558|AY382466.1.1448 into 147|AY204583.1.1843 (99.76% ID over 840 columns) in 0.007 seconds
    ...merging 2559|EF631621.1.1698 into 282|AF525308.1.1700 (97.93% ID over 1591 columns) in 0.002 seconds
    ...merging 2562|AF346492.1.1489 into 1337|EF634451.1.1447 (99.66% ID over 885 columns) in 0.005 seconds
    ...merging 2564|HQ883950.1.1542 into 479|FR877557.4039313.4040854 (99.55% ID over 1119 columns) in 0.010 seconds
    ...merging 2565|EU775130.1.1404 into 1704|EU465480.1.1389 (99.61% ID over 512 columns) in 0.001 seconds
    ...merging 3555|AB622309.1.1677 into 2569|GQ330587.1.1444 (97.45% ID over 628 columns) in 0.000 seconds
    ...merging 3638|AF176565.1.1522 into 2572|AF214639.1.1529 (100.00% ID over 500 columns) in 0.000 seconds
    ...merging 2572|AF214639.1.1529 into 479|FR877557.4039313.4040854 (100.00% ID over 587 columns) in 0.010 seconds
    ...merging 4008|AB243843.1.1507 into 2577|AM493669.1.1377 (99.64% ID over 559 columns) in 0.001 seconds
    ...merging 3337|EU772163.1.1414 into 2577|AM493669.1.1377 (99.83% ID over 576 columns) in 0.000 seconds
    ...merging 4280|EU465948.1.1413 into 2577|AM493669.1.1377 (99.37% ID over 637 columns) in 0.000 seconds
    ...merging 2577|AM493669.1.1377 into 1536|JF346899.1.1511 (99.67% ID over 607 columns) in 0.001 seconds
    ...merging 2584|HQ789849.1.1440 into 479|FR877557.4039313.4040854 (99.23% ID over 1296 columns) in 0.010 seconds
    ...merging 2592|AB695489.1.1762 into 4358|GU067926.1.1792 (100.00% ID over 1056 columns) in 0.001 seconds
    ...merging 2593|DQ278131.1.1663 into 155|DQ278124.1.2101 (98.93% ID over 842 columns) in 0.009 seconds
    ...merging 2596|EU335318.1.1513 into 2117|EF492926.1.1508 (97.78% ID over 809 columns) in 0.001 seconds
    ...merging 2598|HQ739777.1.1441 into 479|FR877557.4039313.4040854 (99.72% ID over 1082 columns) in 0.010 seconds
    ...merging 2601|AY204606.1.1764 into 796|JN397367.1.1797 (98.20% ID over 1330 columns) in 0.003 seconds
    ...merging 2628|ABWE02003231.4031.5360 into 149|M54939.1.1822 (99.65% ID over 570 columns) in 0.006 seconds
    ...merging 2632|AY963387.1.1479 into 3292|EF516775.1.1374 (97.46% ID over 1181 columns) in 0.001 seconds
    ...merging 4221|JN562358.1.1310 into 2634|JN562365.1.1309 (98.69% ID over 609 columns) in 0.000 seconds
    ...merging 2634|JN562365.1.1309 into 155|DQ278124.1.2101 (99.42% ID over 866 columns) in 0.010 seconds
    ...merging 2635|EF024465.1.1809 into 128|FJ869174.1.1779 (97.08% ID over 1473 columns) in 0.002 seconds
    ...merging 2638|AY522887.1.1317 into 257|EU155998.1.1440 (100.00% ID over 618 columns) in 0.004 seconds
    ...merging 2643|EF024775.1.1757 into 1363|EU079472.1.1780 (97.35% ID over 1245 columns) in 0.001 seconds
    ...merging 2648|AF088254.1.1765 into 880|AF274110.1.1754 (97.92% ID over 1296 columns) in 0.001 seconds
    ...merging 2653|HQ880325.1.1466 into 479|FR877557.4039313.4040854 (99.55% ID over 1327 columns) in 0.010 seconds
    ...merging 2657|FJ608656.1.1498 into 479|FR877557.4039313.4040854 (99.60% ID over 990 columns) in 0.010 seconds
    ...merging 2658|GQ406808.1.1696 into 147|AY204583.1.1843 (98.25% ID over 1426 columns) in 0.008 seconds
    ...merging 5176|GU901877.1.1759 into 2662|GU453340.1.1830 (99.33% ID over 1345 columns) in 0.001 seconds
    ...merging 2663|HQ883944.1.1536 into 479|FR877557.4039313.4040854 (99.48% ID over 959 columns) in 0.010 seconds
    ...merging 3249|AM774204.1.1394 into 2665|AM774205.1.1426 (98.89% ID over 903 columns) in 0.001 seconds
    ...merging 2669|AY642701.1.1789 into 447|GQ995332.1.1776 (98.66% ID over 1490 columns) in 0.010 seconds
    ...merging 2670|AE017220.2817349.2818892 into 479|FR877557.4039313.4040854 (99.23% ID over 1038 columns) in 0.010 seconds
    ...merging 2671|AF154566.1.1733 into 324|AB695475.1.1764 (98.58% ID over 984 columns) in 0.001 seconds
    ...merging 2672|ABIS01004081.1.1259 into 1472|GU733366.1.1773 (99.30% ID over 569 columns) in 0.001 seconds
    ...merging 2674|FJ825365.1.1884 into 1108|AY382647.1.1946 (97.21% ID over 1076 columns) in 0.001 seconds
    ...merging 2676|EU420928.1.1346 into 4291|EF669481.1.1458 (99.63% ID over 814 columns) in 0.000 seconds
    ...merging 2681|DQ345467.1.1516 into 3981|HQ436339.1.1499 (99.61% ID over 507 columns) in 0.000 seconds
    ...merging 2682|EF018504.1.1383 into 877|EU861962.1.1512 (98.91% ID over 550 columns) in 0.001 seconds
    ...merging 2686|HQ883956.1.1540 into 479|FR877557.4039313.4040854 (99.38% ID over 971 columns) in 0.010 seconds
    ...merging 2688|FJ686824.1.1357 into 1337|EF634451.1.1447 (98.88% ID over 980 columns) in 0.005 seconds
    ...merging 2697|DQ536481.1.1783 into 2794|AF368504.1.1806 (97.51% ID over 764 columns) in 0.001 seconds
    ...merging 2699|GQ280116.1.1413 into 2208|DQ981817.1.1457 (100.00% ID over 877 columns) in 0.001 seconds
    ...merging 3430|EU335338.1.1530 into 2705|EF516526.1.1465 (98.33% ID over 1016 columns) in 0.000 seconds
    ...merging 2705|EF516526.1.1465 into 3457|EF600558.1.1507 (97.29% ID over 960 columns) in 0.000 seconds
    ...merging 2711|FJ848501.1.1599 into 3052|FJ848488.1.1568 (97.68% ID over 517 columns) in 0.001 seconds
    ...merging 2722|X89868.1.1827 into 5283|EF023522.1.1797 (98.45% ID over 580 columns) in 0.000 seconds
    ...merging 3248|JF145311.1.1352 into 2725|GQ264508.1.1464 (97.94% ID over 970 columns) in 0.000 seconds
    ...merging 2735|GQ493157.1.1380 into 479|FR877557.4039313.4040854 (99.56% ID over 1148 columns) in 0.011 seconds
    ...merging 2737|EU709223.15.1555 into 1232|EU709155.5.1588 (99.03% ID over 1340 columns) in 0.001 seconds
    ...merging 2738|DQ310332.1.1414 into 447|GQ995332.1.1776 (98.89% ID over 542 columns) in 0.010 seconds
    ...merging 2739|L37734.1.3315 into 796|JN397367.1.1797 (98.44% ID over 835 columns) in 0.003 seconds
    ...merging 4511|FJ937901.1.1542 into 2743|AM085483.1.1511 (99.70% ID over 671 columns) in 0.001 seconds
    ...merging 2750|FJ375307.1.1546 into 1408|EF023488.1.1795 (98.49% ID over 1125 columns) in 0.001 seconds
    ...merging 2753|AAAA02048336.579.2089 into 479|FR877557.4039313.4040854 (100.00% ID over 504 columns) in 0.010 seconds
    ...merging 2761|FM958154.1.1263 into 4512|AY603978.1.1435 (99.81% ID over 513 columns) in 0.001 seconds
    ...merging 1933|AF455135.1.1747 into 2765|AF085467.1.1753 (97.00% ID over 967 columns) in 0.001 seconds
    ...merging 2770|Z96084.1.1484 into 479|FR877557.4039313.4040854 (100.00% ID over 632 columns) in 0.010 seconds
    ...merging 2773|CABJ01004404.4432.6221 into 796|JN397367.1.1797 (98.01% ID over 754 columns) in 0.003 seconds
    ...merging 2775|JN562363.1.1309 into 155|DQ278124.1.2101 (99.61% ID over 771 columns) in 0.010 seconds
    ...merging 2780|DQ818874.1.1460 into 479|FR877557.4039313.4040854 (99.69% ID over 1289 columns) in 0.011 seconds
    ...merging 2785|DQ104806.1.1216 into 2|AAXH01001329.94.1810 (97.88% ID over 1084 columns) in 0.043 seconds
    ...merging 2786|EU746414.1.1251 into 3975|JF960957.1.1357 (99.26% ID over 673 columns) in 0.001 seconds
    ...merging 2787|FJ268962.1.1516 into 2788|EU685818.1.1568 (99.87% ID over 750 columns) in 0.000 seconds
    ...merging 3138|DQ448753.1.1514 into 2788|EU685818.1.1568 (99.86% ID over 739 columns) in 0.000 seconds
    ...merging 2794|AF368504.1.1806 into 1099|DQ536471.1.1770 (97.45% ID over 1137 columns) in 0.001 seconds
    ...merging 2796|AY640938.1.1695 into 147|AY204583.1.1843 (99.04% ID over 1255 columns) in 0.008 seconds
    ...merging 2799|AY827952.1.1753 into 324|AB695475.1.1764 (99.86% ID over 724 columns) in 0.001 seconds
    ...merging 2812|EF446895.1.1430 into 3538|HM461182.1.1472 (99.75% ID over 1180 columns) in 0.000 seconds
    ...merging 6785|AF423273.1.1442 into 2819|JN178105.1.1522 (97.59% ID over 623 columns) in 0.000 seconds
    ...merging 6683|EU134978.1.1314 into 2821|EU335449.1.1489 (97.63% ID over 549 columns) in 0.001 seconds
    ...merging 2823|DQ805505.1.1364 into 1704|EU465480.1.1389 (100.00% ID over 522 columns) in 0.000 seconds
    ...merging 4514|FN690503.1.1695 into 2824|AY642695.1.1782 (97.47% ID over 1265 columns) in 0.000 seconds
    ...merging 2826|GU368920.1.1499 into 1337|EF634451.1.1447 (99.92% ID over 1312 columns) in 0.005 seconds
    ...merging 2827|CP001918.5152784.5154334 into 479|FR877557.4039313.4040854 (99.54% ID over 1091 columns) in 0.010 seconds
    ...merging 1571|FM178240.1.1469 into 2835|FM178264.1.1377 (99.07% ID over 1074 columns) in 0.001 seconds
    ...merging 2835|FM178264.1.1377 into 67|X60182.1.1799 (97.67% ID over 1116 columns) in 0.003 seconds
    ...merging 5232|EU135145.1.1384 into 2836|EU135127.1.1377 (98.27% ID over 579 columns) in 0.001 seconds
    ...merging 2964|AY921762.1.1412 into 2836|EU135127.1.1377 (98.51% ID over 670 columns) in 0.000 seconds
    ...merging 2838|AF498729.1.1346 into 1970|HQ674867.1.1493 (98.25% ID over 914 columns) in 0.001 seconds
    ...merging 2840|JN969316.1.1533 into 479|FR877557.4039313.4040854 (99.90% ID over 992 columns) in 0.010 seconds
    ...merging 2842|DQ068760.1.1462 into 479|FR877557.4039313.4040854 (100.00% ID over 961 columns) in 0.010 seconds
    ...merging 2845|AB051892.1.1749 into 2588|AY293132.1.1754 (98.85% ID over 783 columns) in 0.001 seconds
    ...merging 2854|HQ883953.1.1533 into 479|FR877557.4039313.4040854 (99.54% ID over 1082 columns) in 0.010 seconds
    ...merging 2861|AY821917.1.1454 into 1149|DQ411862.1.1642 (98.97% ID over 969 columns) in 0.001 seconds
    ...merging 3799|AY913285.1.1412 into 2862|JN868785.1.1478 (97.64% ID over 1229 columns) in 0.000 seconds
    ...merging 4969|HQ118369.1.1447 into 2862|JN868785.1.1478 (97.62% ID over 839 columns) in 0.000 seconds
    ...merging 2863|FJ805449.1.1330 into 3013|HQ397054.1.1407 (100.00% ID over 645 columns) in 0.000 seconds
    ...merging 2882|HQ759081.1.1395 into 479|FR877557.4039313.4040854 (99.73% ID over 1107 columns) in 0.011 seconds
    ...merging 2883|HQ659713.1.1496 into 2423|EF059868.1.1420 (99.91% ID over 1123 columns) in 0.001 seconds
    ...merging 2884|GQ926883.1.1427 into 1313|FJ217160.1.1446 (99.67% ID over 903 columns) in 0.001 seconds
    ...merging 3227|AJ421685.1.3092 into 2891|AF088240.1.1693 (97.26% ID over 985 columns) in 0.001 seconds
    ...merging 2891|AF088240.1.1693 into 226|JN941185.1.1761 (97.06% ID over 1260 columns) in 0.001 seconds
    ...merging 2895|EF608513.1.1443 into 479|FR877557.4039313.4040854 (100.00% ID over 588 columns) in 0.010 seconds
    ...merging 2899|GQ493993.1.1387 into 1477|EU471193.1.1404 (99.90% ID over 954 columns) in 0.001 seconds
    ...merging 2914|GQ105659.1.1361 into 3538|HM461182.1.1472 (99.72% ID over 1066 columns) in 0.001 seconds
    ...merging 4814|GU067995.1.1774 into 2919|EF024708.1.1779 (97.29% ID over 995 columns) in 0.001 seconds
    ...merging 2923|AY648103.1.2914 into 910|DQ678004.1.1833 (97.72% ID over 1098 columns) in 0.005 seconds
    ...merging 2925|CABJ01000982.2023.3356 into 3056|U53374.1.1656 (99.79% ID over 975 columns) in 0.001 seconds
    ...merging 2926|AF091589.1.1721 into 226|JN941185.1.1761 (97.65% ID over 1062 columns) in 0.001 seconds
    ...merging 5108|GQ272649.1.1472 into 2928|GU339265.1.1360 (99.61% ID over 1030 columns) in 0.000 seconds
    ...merging 5111|DQ988946.1.1443 into 2928|GU339265.1.1360 (99.59% ID over 969 columns) in 0.000 seconds
    ...merging 4035|HQ650161.1.1448 into 2928|GU339265.1.1360 (99.71% ID over 1029 columns) in 0.001 seconds
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    ...merging 2934|DQ336497.1.1233 into 684|AJ699067.1.1793 (97.32% ID over 822 columns) in 0.002 seconds
    ...merging 2946|AY905499.1.2379 into 1051|AM114805.1.2266 (98.39% ID over 993 columns) in 0.001 seconds
    ...merging 2949|HQ844492.1.1429 into 1337|EF634451.1.1447 (99.91% ID over 1161 columns) in 0.005 seconds
    ...merging 2952|U22936.1.1796 into 198|AY220087.1.1792 (99.00% ID over 700 columns) in 0.001 seconds
    ...merging 2956|EU709135.14.1558 into 1232|EU709155.5.1588 (98.15% ID over 974 columns) in 0.001 seconds
    ...merging 4423|AY913402.1.1429 into 2961|EU861842.1.1474 (98.43% ID over 892 columns) in 0.000 seconds
    ...merging 2975|EU742147.1.1458 into 479|FR877557.4039313.4040854 (99.75% ID over 1205 columns) in 0.011 seconds
    ...merging 2977|FR691455.1.1491 into 3981|HQ436339.1.1499 (99.39% ID over 660 columns) in 0.001 seconds
    ...merging 2986|AF412410.1.1717 into 88|EU940018.1.1678 (98.60% ID over 1141 columns) in 0.017 seconds
    ...merging 2988|EU460635.1.1403 into 479|FR877557.4039313.4040854 (99.79% ID over 962 columns) in 0.011 seconds
    ...merging 2993|JF414207.1.1608 into 1099|DQ536471.1.1770 (97.21% ID over 1472 columns) in 0.001 seconds
    ...merging 2994|GU374061.1.1358 into 479|FR877557.4039313.4040854 (98.64% ID over 1319 columns) in 0.010 seconds
    ...merging 2995|AY293147.1.2050 into 5|DQ437679.1.1786 (97.05% ID over 1083 columns) in 0.009 seconds
    ...merging 2999|HE582620.1.1308 into 479|FR877557.4039313.4040854 (99.53% ID over 1284 columns) in 0.011 seconds
    ...merging 3000|HQ791339.1.1461 into 479|FR877557.4039313.4040854 (99.61% ID over 1293 columns) in 0.010 seconds
    ...merging 3001|CU915022.1.1359 into 479|FR877557.4039313.4040854 (99.90% ID over 955 columns) in 0.011 seconds
    ...merging 3003|EU371161.1.1794 into 3922|FJ824121.1.1826 (97.31% ID over 520 columns) in 0.001 seconds
    ...merging 3004|AF372739.1.1278 into 1051|AM114805.1.2266 (99.56% ID over 913 columns) in 0.001 seconds
    ...merging 3027|HQ883935.1.1548 into 479|FR877557.4039313.4040854 (99.19% ID over 859 columns) in 0.011 seconds
    ...merging 3028|DQ244009.1.1790 into 447|GQ995332.1.1776 (98.41% ID over 627 columns) in 0.010 seconds
    ...merging 3029|DQ818882.1.1456 into 479|FR877557.4039313.4040854 (99.42% ID over 1032 columns) in 0.011 seconds
    ...merging 3030|HM013841.1.1412 into 479|FR877557.4039313.4040854 (99.76% ID over 1234 columns) in 0.010 seconds
    ...merging 4231|JN215501.1.1470 into 3041|EU586788.1.1480 (99.40% ID over 831 columns) in 0.001 seconds
    ...merging 3043|CX109058.1.1487 into 4356|ABXC01011031.1.1544 (99.53% ID over 1054 columns) in 0.000 seconds
    ...merging 3047|AB211015.1.1480 into 3981|HQ436339.1.1499 (100.00% ID over 605 columns) in 0.001 seconds
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    ...merging 3052|FJ848488.1.1568 into 441|FJ848507.1.1569 (100.00% ID over 575 columns) in 0.001 seconds
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    ...merging 3057|HM161745.1.1787 into 1212|EF165132.1.1763 (97.91% ID over 959 columns) in 0.001 seconds
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    ...merging 3070|AY388649.1.1360 into 5805|GQ264444.1.1501 (98.75% ID over 722 columns) in 0.000 seconds
    ...merging 3075|AF336898.1.1735 into 147|AY204583.1.1843 (97.04% ID over 945 columns) in 0.008 seconds
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    ...merging 3086|U20275.1.1508 into 479|FR877557.4039313.4040854 (98.86% ID over 704 columns) in 0.011 seconds
    ...merging 3090|EF516009.1.1412 into 4111|FJ478985.1.1458 (97.48% ID over 714 columns) in 0.001 seconds
    ...merging 3099|EU132881.1.1325 into 1979|HQ119173.1.1519 (98.33% ID over 897 columns) in 0.001 seconds
    ...merging 3100|GU366042.1.1200 into 1313|FJ217160.1.1446 (100.00% ID over 836 columns) in 0.001 seconds
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    ...merging 2833|EU773800.1.1399 into 3115|GQ867427.1.1505 (100.00% ID over 618 columns) in 0.001 seconds
    ...merging 3115|GQ867427.1.1505 into 479|FR877557.4039313.4040854 (100.00% ID over 740 columns) in 0.011 seconds
    ...merging 3119|EF100203.1.1580 into 190|GU070876.1.1792 (99.65% ID over 867 columns) in 0.004 seconds
    ...merging 3120|GU324769.1.1449 into 479|FR877557.4039313.4040854 (99.84% ID over 1240 columns) in 0.011 seconds
    ...merging 3123|AY821976.1.1591 into 149|M54939.1.1822 (97.04% ID over 1216 columns) in 0.006 seconds
    ...merging 3126|HQ844462.1.1439 into 1337|EF634451.1.1447 (100.00% ID over 1014 columns) in 0.005 seconds
    ...merging 3131|X89870.1.1827 into 3302|X78889.1.1811 (97.10% ID over 1138 columns) in 0.001 seconds
    ...merging 3133|AY593917.1.1701 into 3421|AY284635.1.1741 (97.08% ID over 719 columns) in 0.001 seconds
    ...merging 3134|AF441172.1.1708 into 162|AY518668.1.1777 (98.35% ID over 1392 columns) in 0.005 seconds
    ...merging 4228|EU469346.1.1363 into 3143|EU465926.1.1412 (99.64% ID over 553 columns) in 0.001 seconds
    ...merging 5469|HM062466.1.1419 into 3153|AB179518.1.1464 (98.07% ID over 1189 columns) in 0.000 seconds
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    ...merging 3168|AY563462.1.1565 into 479|FR877557.4039313.4040854 (99.48% ID over 967 columns) in 0.011 seconds
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    ...merging 4810|GU374094.1.1366 into 3176|DQ816137.1.1330 (99.87% ID over 776 columns) in 0.001 seconds
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    ...merging 3179|AY642710.1.1346 into 2569|GQ330587.1.1444 (97.61% ID over 838 columns) in 0.000 seconds
    ...merging 4417|GQ264207.1.1477 into 3181|GQ264237.1.1474 (97.59% ID over 790 columns) in 0.000 seconds
    ...merging 3181|GQ264237.1.1474 into 304|EF019302.1.1385 (97.59% ID over 953 columns) in 0.001 seconds
    ...merging 3209|DQ910903.1.1717 into 1363|EU079472.1.1780 (99.53% ID over 857 columns) in 0.001 seconds
    ...merging 3212|EU302833.1.1463 into 479|FR877557.4039313.4040854 (99.65% ID over 1132 columns) in 0.011 seconds
    ...merging 3224|EU940021.1.1679 into 910|DQ678004.1.1833 (98.02% ID over 1215 columns) in 0.005 seconds
    ...merging 3231|FJ405282.1.1504 into 479|FR877557.4039313.4040854 (99.19% ID over 865 columns) in 0.011 seconds
    ...merging 3232|EU335232.1.1491 into 4262|EF019422.1.1396 (97.02% ID over 806 columns) in 0.001 seconds
    ...merging 3237|EU133174.1.1410 into 1979|HQ119173.1.1519 (99.53% ID over 858 columns) in 0.001 seconds
    ...merging 6996|EF024430.1.1795 into 3240|EF024365.1.1785 (98.58% ID over 914 columns) in 0.000 seconds
    ...merging 3254|FJ440555.1.1421 into 2423|EF059868.1.1420 (99.91% ID over 1092 columns) in 0.001 seconds
    ...merging 5109|HQ118388.1.1453 into 3256|HQ132473.1.1492 (98.01% ID over 854 columns) in 0.000 seconds
    ...merging 4695|FR853451.1.1447 into 3256|HQ132473.1.1492 (97.08% ID over 686 columns) in 0.000 seconds
    ...merging 3260|AJ421680.1.1748 into 796|JN397367.1.1797 (97.54% ID over 1583 columns) in 0.004 seconds
    ...merging 3268|AJ315168.1.1693 into 1472|GU733366.1.1773 (97.19% ID over 996 columns) in 0.001 seconds
    ...merging 3304|DQ873611.1.1772 into 5|DQ437679.1.1786 (97.39% ID over 804 columns) in 0.009 seconds
    ...merging 3312|GU067821.1.1606 into 1036|AJ781312.1.1776 (98.39% ID over 746 columns) in 0.001 seconds
    ...merging 3325|HQ759066.1.1466 into 479|FR877557.4039313.4040854 (99.45% ID over 1262 columns) in 0.011 seconds
    ...merging 3327|FJ466236.1.1455 into 3542|AY913229.1.1448 (97.04% ID over 979 columns) in 0.001 seconds
    ...merging 3334|DQ298003.1.1421 into 3890|FJ466095.1.1398 (98.25% ID over 856 columns) in 0.000 seconds
    ...merging 3340|FN667520.1.1484 into 1940|AY082367.1.1576 (99.85% ID over 686 columns) in 0.001 seconds
    ...merging 5933|EF516100.1.1454 into 3350|HQ119291.1.1498 (98.65% ID over 1262 columns) in 0.000 seconds
    ...merging 3353|HQ844494.1.1438 into 1337|EF634451.1.1447 (100.00% ID over 702 columns) in 0.005 seconds
    ...merging 3354|AY779282.1.1617 into 4562|AF113720.1.1688 (98.82% ID over 930 columns) in 0.001 seconds
    ...merging 3362|EU771598.1.1401 into 1592|GQ867431.1.1483 (99.80% ID over 507 columns) in 0.001 seconds
    ...merging 3368|EF465457.1.1467 into 2208|DQ981817.1.1457 (98.94% ID over 947 columns) in 0.001 seconds
    ...merging 3372|JQ315893.1.1498 into 479|FR877557.4039313.4040854 (98.31% ID over 830 columns) in 0.011 seconds
    ...merging 3375|D86910.1.1704 into 67|X60182.1.1799 (99.14% ID over 1161 columns) in 0.003 seconds
    ...merging 3379|HQ787553.1.1458 into 479|FR877557.4039313.4040854 (99.67% ID over 602 columns) in 0.011 seconds
    ...merging 3390|EF644419.3.1455 into 105|EU780733.1.1447 (99.77% ID over 854 columns) in 0.003 seconds
    ...merging 3843|HQ119004.1.1321 into 3391|HQ118429.1.1486 (98.54% ID over 1165 columns) in 0.001 seconds
    ...merging 6956|HQ219393.1.2359 into 3392|EF023892.1.1780 (97.78% ID over 946 columns) in 0.000 seconds
    ...merging 3392|EF023892.1.1780 into 198|AY220087.1.1792 (97.48% ID over 755 columns) in 0.001 seconds
    ...merging 3393|EU777743.1.1313 into 1351|EU777753.1.1312 (99.83% ID over 592 columns) in 0.001 seconds
    ...merging 3394|AJ315056.1.1522 into 1706|JF802176.1.1486 (99.79% ID over 939 columns) in 0.001 seconds
    ...merging 3407|HM582877.1.1446 into 3538|HM461182.1.1472 (99.87% ID over 762 columns) in 0.000 seconds
    ...merging 3408|FJ228149.1.1232 into 1536|JF346899.1.1511 (100.00% ID over 791 columns) in 0.001 seconds
    ...merging 3989|U71196.1.1787 into 3409|AF123302.1.1790 (99.16% ID over 836 columns) in 0.000 seconds
    ...merging 3414|JN411304.1.1292 into 1219|DQ323076.1.1455 (100.00% ID over 1113 columns) in 0.001 seconds
    ...merging 3432|JF730766.1.1687 into 507|AB520733.1.1665 (97.84% ID over 1157 columns) in 0.001 seconds
    ...merging 3434|EU407552.1.1427 into 3484|HQ443224.1.1463 (99.88% ID over 821 columns) in 0.001 seconds
    ...merging 3437|AF372763.1.1585 into 149|M54939.1.1822 (99.39% ID over 1155 columns) in 0.007 seconds
    ...merging 5738|AB698779.1.1541 into 3453|GQ284390.1.1473 (99.70% ID over 668 columns) in 0.001 seconds
    ...merging 3463|FJ824051.1.1314 into 337|HQ118984.1.1488 (98.15% ID over 1187 columns) in 0.001 seconds
    ...merging 3465|FJ607347.1.1440 into 1706|JF802176.1.1486 (99.85% ID over 676 columns) in 0.001 seconds
    ...merging 4377|AB566415.1.1535 into 3466|FJ849420.1.1465 (99.46% ID over 557 columns) in 0.000 seconds
    ...merging 3477|EU360881.1.1628 into 226|JN941185.1.1761 (98.21% ID over 1343 columns) in 0.001 seconds
    ...merging 3478|FJ796221.1.1407 into 479|FR877557.4039313.4040854 (99.81% ID over 1034 columns) in 0.011 seconds
    ...merging 3484|HQ443224.1.1463 into 1706|JF802176.1.1486 (100.00% ID over 972 columns) in 0.001 seconds
    ...merging 3487|EF443134.1.1652 into 447|GQ995332.1.1776 (97.53% ID over 849 columns) in 0.010 seconds
    ...merging 3488|EF102824.1.1455 into 479|FR877557.4039313.4040854 (99.84% ID over 1221 columns) in 0.011 seconds
    ...merging 3490|JF343143.1.1436 into 1337|EF634451.1.1447 (99.91% ID over 1071 columns) in 0.005 seconds
    ...merging 4356|ABXC01011031.1.1544 into 3491|ABXC01012396.796.2573 (99.92% ID over 1288 columns) in 0.001 seconds
    ...merging 4457|AAAA02041579.2617.4209 into 3491|ABXC01012396.796.2573 (99.29% ID over 1269 columns) in 0.000 seconds
    ...merging 3492|AF455133.1.1669 into 910|DQ678004.1.1833 (97.47% ID over 751 columns) in 0.005 seconds
    ...merging 3493|EU445222.1.1509 into 4705|AY913233.1.1441 (100.00% ID over 870 columns) in 0.001 seconds
    ...merging 3500|FM208262.1.1439 into 6029|GU130113.1.1483 (97.25% ID over 509 columns) in 0.000 seconds
    ...merging 3502|EU121410.1.1576 into 479|FR877557.4039313.4040854 (99.88% ID over 801 columns) in 0.011 seconds
    ...merging 3517|EF682459.1.1356 into 104|GU187637.1.1624 (99.48% ID over 572 columns) in 0.002 seconds
    ...merging 3519|JN676212.1.1471 into 1337|EF634451.1.1447 (99.55% ID over 888 columns) in 0.005 seconds
    ...merging 3533|EU133108.1.1387 into 2117|EF492926.1.1508 (97.59% ID over 995 columns) in 0.001 seconds
    ...merging 3535|GQ402551.1.1433 into 4588|HM270010.1.1330 (99.67% ID over 896 columns) in 0.000 seconds
    ...merging 3544|JN098699.1.1467 into 1337|EF634451.1.1447 (99.83% ID over 1211 columns) in 0.005 seconds
    ...merging 3562|JN626195.1.1493 into 479|FR877557.4039313.4040854 (99.44% ID over 1078 columns) in 0.011 seconds
    ...merging 3572|EU162638.1.1788 into 5220|JF972676.1.1641 (97.00% ID over 534 columns) in 0.001 seconds
    ...merging 3575|GU820981.1.1215 into 1830|AB695472.1.1770 (97.28% ID over 771 columns) in 0.001 seconds
    ...merging 3580|HM159968.1.1503 into 479|FR877557.4039313.4040854 (99.59% ID over 1220 columns) in 0.011 seconds
    ...merging 3598|GU727722.1.1508 into 4663|GU172185.1.1520 (99.43% ID over 872 columns) in 0.001 seconds
    ...merging 3600|EF516307.1.1378 into 3391|HQ118429.1.1486 (98.29% ID over 1108 columns) in 0.000 seconds
    ...merging 3614|FJ891034.1.1403 into 1979|HQ119173.1.1519 (98.27% ID over 1388 columns) in 0.001 seconds
    ...merging 3618|HM461143.1.1466 into 3773|HM461202.1.1469 (99.55% ID over 1099 columns) in 0.000 seconds
    ...merging 3622|EF492909.1.1461 into 5130|HM062270.1.1418 (100.00% ID over 1278 columns) in 0.000 seconds
    ...merging 3652|HQ767557.1.1413 into 1535|HQ757360.1.1423 (99.86% ID over 703 columns) in 0.001 seconds
    ...merging 3661|HQ419280.1.1500 into 1272|JF043143.1.1362 (99.46% ID over 736 columns) in 0.001 seconds
    ...merging 3668|HQ883928.1.1598 into 479|FR877557.4039313.4040854 (99.43% ID over 1052 columns) in 0.011 seconds
    ...merging 3675|AF088237.1.1740 into 796|JN397367.1.1797 (98.68% ID over 1138 columns) in 0.004 seconds
    ...merging 3688|HM556133.1.1388 into 479|FR877557.4039313.4040854 (97.98% ID over 1087 columns) in 0.011 seconds
    ...merging 3690|DQ273686.1.1220 into 4001|FJ823009.1.1399 (99.69% ID over 635 columns) in 0.001 seconds
    ...merging 3703|EF024107.1.1777 into 214|EF024888.1.1775 (99.12% ID over 1142 columns) in 0.001 seconds
    ...merging 3723|EU778441.1.1402 into 479|FR877557.4039313.4040854 (99.88% ID over 852 columns) in 0.011 seconds
    ...merging 3725|AY654882.1.1678 into 40|AEQB01000388.114521.116319 (98.65% ID over 1334 columns) in 0.004 seconds
    ...merging 3731|EU709203.14.1561 into 1232|EU709155.5.1588 (97.16% ID over 1268 columns) in 0.001 seconds
    ...merging 2729|FM162181.1.1490 into 3733|AB637131.1.1509 (99.44% ID over 900 columns) in 0.000 seconds
    ...merging 2743|AM085483.1.1511 into 3733|AB637131.1.1509 (99.82% ID over 541 columns) in 0.001 seconds
    ...merging 3743|HQ219429.1.2348 into 2492|EF024441.1.1845 (97.84% ID over 742 columns) in 0.000 seconds
    ...merging 3747|AY919752.1.1722 into 91|EF023425.1.1776 (98.56% ID over 1454 columns) in 0.002 seconds
    ...merging 3758|EF025245.1.1450 into 969|EU723861.1.1508 (99.82% ID over 566 columns) in 0.001 seconds
    ...merging 3768|DQ988943.1.1453 into 3538|HM461182.1.1472 (100.00% ID over 556 columns) in 0.001 seconds
    ...merging 3773|HM461202.1.1469 into 2423|EF059868.1.1420 (99.66% ID over 1186 columns) in 0.001 seconds
    ...merging 3776|EU360869.1.1341 into 814|DQ471002.1.1574 (98.16% ID over 1141 columns) in 0.001 seconds
    ...merging 3786|AY382472.1.1445 into 360|DQ457626.1.1789 (99.48% ID over 579 columns) in 0.001 seconds
    ...merging 3787|EU742143.1.1515 into 3538|HM461182.1.1472 (99.79% ID over 943 columns) in 0.001 seconds
    ...merging 3790|AB695447.1.1738 into 1363|EU079472.1.1780 (98.76% ID over 970 columns) in 0.001 seconds
    ...merging 3794|AY179978.1.1785 into 1363|EU079472.1.1780 (100.00% ID over 762 columns) in 0.001 seconds
    ...merging 3796|HM461134.1.1466 into 4897|HM461126.1.1463 (100.00% ID over 758 columns) in 0.000 seconds
    ...merging 3813|AF534712.1.2943 into 2857|AB695523.1.1762 (98.09% ID over 1098 columns) in 0.001 seconds
    ...merging 3815|JF920340.1.1383 into 1372|EU777805.1.1431 (100.00% ID over 639 columns) in 0.001 seconds
    ...merging 3835|FJ386544.1.1352 into 1337|EF634451.1.1447 (99.75% ID over 1204 columns) in 0.005 seconds
    ...merging 3842|AY620311.1.1258 into 2266|DQ369017.1.1820 (97.58% ID over 537 columns) in 0.001 seconds
    ...merging 3845|EF612393.1.1486 into 4383|AM934876.1.1373 (98.68% ID over 604 columns) in 0.000 seconds
    ...merging 3862|AY916577.1.1855 into 507|AB520733.1.1665 (99.58% ID over 714 columns) in 0.001 seconds
    ...merging 3874|HQ009753.1.1434 into 1337|EF634451.1.1447 (100.00% ID over 572 columns) in 0.005 seconds
    ...merging 3881|JN562361.1.1308 into 389|AY522878.1.1316 (98.98% ID over 587 columns) in 0.001 seconds
    ...merging 3895|JN119828.1.1447 into 2165|EU124827.1.1502 (99.68% ID over 627 columns) in 0.001 seconds
    ...merging 3908|EF526922.1.1254 into 1089|EF024143.1.1792 (98.85% ID over 1046 columns) in 0.001 seconds
    ...merging 3913|FJ516885.1.1518 into 2555|FJ268976.1.1516 (100.00% ID over 789 columns) in 0.001 seconds
    ...merging 3914|AF227845.1.1418 into 479|FR877557.4039313.4040854 (99.57% ID over 932 columns) in 0.011 seconds
    ...merging 3924|GU057051.1.1500 into 2208|DQ981817.1.1457 (99.79% ID over 940 columns) in 0.001 seconds
    ...merging 3931|FJ368331.1.1375 into 1435|EU471064.1.1403 (99.14% ID over 817 columns) in 0.001 seconds
    ...merging 3938|JN086487.1.1633 into 1756|HQ188962.1.1693 (97.64% ID over 1230 columns) in 0.001 seconds
    ...merging 3940|AJ131786.1.1741 into 1472|GU733366.1.1773 (98.18% ID over 1152 columns) in 0.001 seconds
    ...merging 3961|HQ844262.1.1487 into 479|FR877557.4039313.4040854 (99.17% ID over 1198 columns) in 0.011 seconds
    ...merging 3975|JF960957.1.1357 into 2208|DQ981817.1.1457 (99.49% ID over 973 columns) in 0.001 seconds
    ...merging 3976|JN635493.1.1268 into 1096|EF023460.1.1914 (99.28% ID over 694 columns) in 0.001 seconds
    ...merging 3981|HQ436339.1.1499 into 1940|AY082367.1.1576 (99.49% ID over 583 columns) in 0.001 seconds
    ...merging 3995|EU471304.1.1327 into 479|FR877557.4039313.4040854 (99.82% ID over 556 columns) in 0.011 seconds
    ...merging 3996|JF783991.1.1454 into 479|FR877557.4039313.4040854 (99.85% ID over 1309 columns) in 0.011 seconds
    ...merging 4000|GQ097541.1.1363 into 479|FR877557.4039313.4040854 (99.76% ID over 1272 columns) in 0.011 seconds
    ...merging 3538|HM461182.1.1472 into 4001|FJ823009.1.1399 (100.00% ID over 1261 columns) in 0.001 seconds
    ...merging 4010|EU778426.1.1385 into 4793|EU775607.1.1374 (99.82% ID over 550 columns) in 0.001 seconds
    ...merging 4014|GQ264277.1.1473 into 304|EF019302.1.1385 (97.66% ID over 899 columns) in 0.001 seconds
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    ...merging 4049|AF026626.1.1779 into 597|U59082.1.1815 (98.56% ID over 836 columns) in 0.001 seconds
    ...merging 4051|EU417644.1.1286 into 684|AJ699067.1.1793 (99.40% ID over 839 columns) in 0.002 seconds
    ...merging 4068|Y18699.1.1632 into 796|JN397367.1.1797 (97.14% ID over 1258 columns) in 0.003 seconds
    ...merging 4085|AB084601.1.1682 into 2588|AY293132.1.1754 (98.79% ID over 1153 columns) in 0.001 seconds
    ...merging 6466|FN820274.1.1771 into 4117|AM183923.1.1769 (98.06% ID over 516 columns) in 0.000 seconds
    ...merging 4131|AF026639.1.1790 into 597|U59082.1.1815 (97.19% ID over 854 columns) in 0.001 seconds
    ...merging 4144|AF184749.1.1687 into 3035|AF117981.1.1798 (97.13% ID over 1148 columns) in 0.001 seconds
    ...merging 4173|AF021794.1.1743 into 95|AB278186.1.2200 (97.08% ID over 1026 columns) in 0.062 seconds
    ...merging 4184|FJ885037.1.1363 into 2391|EU778496.1.1401 (99.33% ID over 751 columns) in 0.001 seconds
    ...merging 2808|GQ407160.1.1434 into 4202|JF835115.1.1241 (99.87% ID over 792 columns) in 0.001 seconds
    ...merging 3476|HM557571.1.1351 into 4243|CU915079.1.1330 (99.82% ID over 552 columns) in 0.000 seconds
    ...merging 4243|CU915079.1.1330 into 479|FR877557.4039313.4040854 (100.00% ID over 617 columns) in 0.012 seconds
    ...merging 4262|EF019422.1.1396 into 1926|JF429126.1.1537 (97.99% ID over 996 columns) in 0.001 seconds
    ...merging 4273|AJ277569.1.1509 into 6029|GU130113.1.1483 (97.71% ID over 700 columns) in 0.000 seconds
    ...merging 6315|X74005.1.1792 into 4287|X56100.1.2186 (97.77% ID over 583 columns) in 0.000 seconds
    ...merging 4304|GQ280059.1.1440 into 4139|GQ927166.1.1427 (99.64% ID over 551 columns) in 0.000 seconds
    ...merging 4343|EU586324.1.1444 into 3139|FJ957661.1.1478 (99.73% ID over 749 columns) in 0.000 seconds
    ...merging 4396|AF026601.1.1720 into 5|DQ437679.1.1786 (98.41% ID over 1071 columns) in 0.009 seconds
    ...merging 4402|GQ352407.1.1221 into 1706|JF802176.1.1486 (99.84% ID over 643 columns) in 0.001 seconds
    ...merging 4413|HQ455823.1.1549 into 479|FR877557.4039313.4040854 (99.27% ID over 1226 columns) in 0.011 seconds
    ...merging 4415|JN698646.1.1438 into 2423|EF059868.1.1420 (98.58% ID over 844 columns) in 0.001 seconds
    ...merging 4271|HE576037.1.1393 into 4416|EU560762.1.1501 (99.84% ID over 635 columns) in 0.000 seconds
    ...merging 4436|EU133151.1.1278 into 877|EU861962.1.1512 (98.16% ID over 979 columns) in 0.001 seconds
    ...merging 4441|AY520225.1.1751 into 147|AY204583.1.1843 (98.32% ID over 716 columns) in 0.008 seconds
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    ...merging 4512|AY603978.1.1435 into 1706|JF802176.1.1486 (100.00% ID over 726 columns) in 0.001 seconds
    ...merging 4521|GU824234.1.1200 into 2609|AB035895.1.2133 (98.34% ID over 905 columns) in 0.001 seconds
    ...merging 4541|AY642706.1.1401 into 939|EU162640.1.1784 (98.43% ID over 826 columns) in 0.000 seconds
    ...merging 988|JN082684.1.1541 into 4554|EF653420.1.1493 (99.01% ID over 608 columns) in 0.001 seconds
    ...merging 4562|AF113720.1.1688 into 226|JN941185.1.1761 (98.13% ID over 1015 columns) in 0.001 seconds
    ...merging 4564|CU915025.1.1334 into 479|FR877557.4039313.4040854 (99.79% ID over 972 columns) in 0.011 seconds
    ...merging 4579|AB362281.1.1416 into 3733|AB637131.1.1509 (99.59% ID over 736 columns) in 0.001 seconds
    ...merging 4687|AJ318168.1.1503 into 4612|JN038942.1.1513 (99.85% ID over 669 columns) in 0.000 seconds
    ...merging 5740|FJ004645.1.1335 into 4612|JN038942.1.1513 (99.63% ID over 809 columns) in 0.000 seconds
    ...merging 4648|EU775002.1.1308 into 1834|EU776680.1.1401 (100.00% ID over 522 columns) in 0.001 seconds
    ...merging 4105|AY941839.1.1537 into 4657|EU430752.1.1495 (100.00% ID over 686 columns) in 0.000 seconds
    ...merging 4668|GQ088231.1.1338 into 6873|DQ448720.1.1484 (97.94% ID over 678 columns) in 0.000 seconds
    ...merging 4720|GU070861.1.1746 into 1363|EU079472.1.1780 (97.78% ID over 1037 columns) in 0.001 seconds
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    ...merging 4744|FJ169947.1.1510 into 2208|DQ981817.1.1457 (100.00% ID over 519 columns) in 0.001 seconds
    ...merging 4781|EU135253.1.1360 into 2014|JN867703.1.1370 (98.14% ID over 700 columns) in 0.001 seconds
    ...merging 4802|AAAA02020713.1.1297 into 479|FR877557.4039313.4040854 (99.65% ID over 572 columns) in 0.011 seconds
    ...merging 6800|FJ466073.1.1398 into 4835|FR749820.1.1463 (99.32% ID over 1035 columns) in 0.001 seconds
    ...merging 4847|HM756474.1.1242 into 2208|DQ981817.1.1457 (99.86% ID over 709 columns) in 0.001 seconds
    ...merging 4868|HM216563.1.1227 into 1337|EF634451.1.1447 (100.00% ID over 579 columns) in 0.005 seconds
    ...merging 4874|FJ957785.1.1516 into 5062|FJ957793.1.1519 (99.81% ID over 535 columns) in 0.001 seconds
    ...merging 4882|JN562342.1.1309 into 448|U62816.1.1402 (98.03% ID over 1064 columns) in 0.001 seconds
    ...merging 4897|HM461126.1.1463 into 2423|EF059868.1.1420 (99.91% ID over 1127 columns) in 0.001 seconds
    ...merging 4912|DQ534692.1.1780 into 40|AEQB01000388.114521.116319 (98.78% ID over 820 columns) in 0.004 seconds
    ...merging 4915|EU294010.1.1408 into 1752|EF422864.1.1474 (99.84% ID over 1218 columns) in 0.001 seconds
    ...merging 4979|AY723697.1.1287 into 2208|DQ981817.1.1457 (99.87% ID over 756 columns) in 0.001 seconds
    ...merging 5022|HQ844515.1.1448 into 1337|EF634451.1.1447 (99.81% ID over 1075 columns) in 0.005 seconds
    ...merging 5072|FJ536892.1.1449 into 304|EF019302.1.1385 (97.41% ID over 888 columns) in 0.001 seconds
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    ...merging 5107|HM569264.1.1621 into 1363|EU079472.1.1780 (98.60% ID over 1211 columns) in 0.002 seconds
    ...merging 5188|AF327397.1.1237 into 145|EF211127.1.2337 (99.43% ID over 700 columns) in 0.010 seconds
    ...merging 6194|JN409180.1.1439 into 5253|HQ674846.1.1508 (99.38% ID over 810 columns) in 0.001 seconds
    ...merging 5270|M90826.1.1208 into 40|AEQB01000388.114521.116319 (98.53% ID over 747 columns) in 0.004 seconds
    ...merging 5296|FJ477666.1.1463 into 479|FR877557.4039313.4040854 (100.00% ID over 790 columns) in 0.012 seconds
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    ...merging 5326|HM262794.1.1368 into 1979|HQ119173.1.1519 (99.57% ID over 938 columns) in 0.001 seconds
    ...merging 5371|DQ336493.1.1236 into 684|AJ699067.1.1793 (99.22% ID over 774 columns) in 0.002 seconds
    ...merging 5398|HQ696567.1.1266 into 1830|AB695472.1.1770 (97.02% ID over 604 columns) in 0.001 seconds
    ...merging 5409|AB504755.1.1442 into 479|FR877557.4039313.4040854 (99.81% ID over 1052 columns) in 0.012 seconds
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    ...merging 5436|FR870447.1.1508 into 479|FR877557.4039313.4040854 (99.68% ID over 926 columns) in 0.011 seconds
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    ...merging 5612|AY284679.1.1600 into 752|EU306344.1.1800 (97.94% ID over 1115 columns) in 0.002 seconds
    ...merging 5666|FJ975934.1.1349 into 3385|GQ156457.1.1356 (98.38% ID over 741 columns) in 0.001 seconds
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    ...merging 5816|FJ751910.1.1496 into 2334|GQ926886.1.1538 (99.44% ID over 714 columns) in 0.001 seconds
    ...merging 5828|EF682466.1.1360 into 1408|EF023488.1.1795 (97.69% ID over 864 columns) in 0.001 seconds
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    ...merging 5929|EF023180.1.1787 into 833|EF024163.1.1795 (98.22% ID over 563 columns) in 0.000 seconds
    ...merging 5973|GU325515.1.1686 into 91|EF023425.1.1776 (99.80% ID over 1007 columns) in 0.001 seconds
    ...merging 5980|EF019407.1.1393 into 1226|EU677394.1.1470 (97.88% ID over 565 columns) in 0.001 seconds
    ...merging 5983|GU822568.1.1215 into 253|AB695519.1.1774 (97.09% ID over 755 columns) in 0.001 seconds
    ...merging 6011|AB520721.1.1709 into 507|AB520733.1.1665 (99.16% ID over 948 columns) in 0.001 seconds
    ...merging 6030|AF276988.1.1394 into 1674|GQ417249.1.1463 (100.00% ID over 602 columns) in 0.000 seconds
    ...merging 6033|DQ450690.1.1301 into 3715|EF516655.1.1423 (97.31% ID over 632 columns) in 0.000 seconds
    ...merging 6038|EU408775.1.1296 into 140|AY245674.1.1971 (98.66% ID over 747 columns) in 0.005 seconds
    ...merging 6048|EU560770.1.1499 into 479|FR877557.4039313.4040854 (99.53% ID over 637 columns) in 0.011 seconds
    ...merging 6052|EF526803.1.1334 into 445|EF023967.1.1849 (98.60% ID over 641 columns) in 0.009 seconds
    ...merging 6132|EF565163.1.1724 into 447|GQ995332.1.1776 (97.27% ID over 1027 columns) in 0.010 seconds
    ...merging 6151|AB275090.1.1653 into 507|AB520733.1.1665 (98.92% ID over 922 columns) in 0.001 seconds
    ...merging 3424|GU377281.1.1502 into 6205|GQ375782.1.1416 (100.00% ID over 524 columns) in 0.000 seconds
    ...merging 6269|ABWL02000011.84303.85559 into 479|FR877557.4039313.4040854 (99.07% ID over 1076 columns) in 0.011 seconds
    ...merging 6282|AY620350.1.1265 into 1547|FJ824128.1.1822 (97.88% ID over 945 columns) in 0.001 seconds
    ...merging 6329|EU133242.1.1400 into 3548|FJ479001.1.1505 (98.76% ID over 646 columns) in 0.000 seconds
    ...merging 6464|EU778802.1.1357 into 1536|JF346899.1.1511 (100.00% ID over 687 columns) in 0.001 seconds
    ...merging 6517|HM557278.1.1374 into 742|GX182404.8.1529 (99.88% ID over 802 columns) in 0.001 seconds
    ...merging 7264|AY345450.1.1356 into 2208|DQ981817.1.1457 (99.71% ID over 686 columns) in 0.001 seconds
    ...merging 7866|AB368994.1.1347 into 479|FR877557.4039313.4040854 (99.23% ID over 915 columns) in 0.012 seconds
    ...merging 12019|AF346542.1.1312_m01 into 12034|AF431948.1.1703_m01 (97.10% ID over 930 columns) in 0.002 seconds
    ...merging 12028|DQ076324.1.1967_m01 into 1|AAFU01000611.1545.3345 (97.67% ID over 1414 columns) in 0.378 seconds
    ...merging 12010|EU159531.1.1574_m01 into 12033|EU847666.1.1272_m01 (97.38% ID over 1185 columns) in 0.003 seconds
    ...merging 12090|FJ358317.1.1590_m01 into 12041|FJ358333.1.1599_m01 (97.08% ID over 1473 columns) in 0.002 seconds
    ...merging 12060|AY315424.1.2219_m01 into 411|HQ219403.1.2424 (97.21% ID over 1327 columns) in 0.010 seconds
    ...merging 12085|DQ851575.1.1788_m01 into 5|DQ437679.1.1786 (97.02% ID over 1610 columns) in 0.009 seconds
Writing new fasta file for iteration 0 at Tue Apr 12 23:37:42 2016...
    removed 2132 sequences after merging
    sequences remaining for iteration 00: 1242
DONE Clustering sequences for iteration 0 at Tue Apr 12 23:37:43 2016 [0:00:59.205856]...
Writing priors and probN to disk for iteration 0 at Tue Apr 12 23:37:43 2016...
DONE Writing priors and probN to disk for iteration 0 at Tue Apr 12 23:37:46 2016...
Starting read mapping for iteration 0 at Tue Apr 12 23:37:46 2016...
    bowtie-build command:
    bowtie-build -o 3 /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/EMIRGE_output/iter.00/iter.00.cons.fasta /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/EMIRGE_output/iter.00/bowtie.index.iter.00 > /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/EMIRGE_output/iter.00/bowtie.iter.00.log 2>&1
    bowtie command:
    cat  /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/B_R1_cd_out_fastq |  bowtie --phred33-quals -t -p 1  -n 3 -l 20 -e 300  --best --strata --all --sam --chunkmbs 128 --minins 295 --maxins 637 /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/EMIRGE_output/iter.00/bowtie.index.iter.00 -1 - -2 /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/B_R2_cd_out_fastq | samtools view -b -S -F 0x0004 - > /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/EMIRGE_output/iter.00/bowtie.iter.00.PE.bam 2> /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/EMIRGE_output/iter.00/bowtie.iter.00.log

Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00

Seeded quality full-index search: 09:35:16
# reads processed: 35174859
# reads with at least one reported alignment: 3057707 (8.69%)
# reads that failed to align: 32117152 (91.31%)
Reported 45746679 paired-end alignments to 1 output stream(s)
Time searching: 09:35:16
Overall time: 09:35:16
    Finished Bowtie for iteration 00 at Wed Apr 13 09:13:09 2016:
DONE with read mapping for iteration 0 at Wed Apr 13 09:13:10 2016...
Finished iteration 0 at Wed Apr 13 09:13:10 2016...
Total time for iteration 0: 9:41:09.488352
Starting iteration 1 at Wed Apr 13 09:13:10 2016...
Reading bam file /media/colemanderrlab/workspace/Ling/MetaT_data_clean/Clean_Fastq/EMIRGE_output/iter.00/bowtie.iter.00.PE.bam at Wed Apr 13 09:13:10 2016...
[fai_load] build FASTA index.
Killed

Best,

Ling