usearch error?
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Cyrus Zhou
Jan 30, 2017, 7:32:55 PM1/30/17
to EMIRGE users
Hello,
I am a first time EMIRGE user. I am not sure what the bug is here, I was hoping you can help.
Command:
~/Desktop/CZ/EMIRGE-master/emirge.py -1 abbr_I19B2_R1.fastq -2 abbr_I19B2_R2.fastq -f ~/Desktop/CZ/EMIRGE-master/SI*fasta -b ~/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 160 -i 217 -s 53 --phred33 19B_EMIRGE_output/
Output:
imported _emirge C functions from: /home/czhou.MI/.cache/Python-Eggs/EMIRGE-0.61.0-py2.7-linux-x86_64.egg-tmp/_emirge.so
Command:
/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py -1 abbr_I19B2_R1.fastq -2 abbr_I19B2_R2.fastq -f /home/czhou.MI/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -b /home/czhou.MI/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 160 -i 217 -s 53 --phred33 19B_EMIRGE_output/
EMIRGE started at Mon Jan 30 13:12:02 2017
Performing initial mapping with command:
cat /home/czhou.MI/Desktop/CZ/CZBins/abbr_I19B2_R1.fastq | bowtie --phred33-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128 --minins 160 --maxins 376 /home/czhou.MI/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -1 - -2 /home/czhou.MI/Desktop/CZ/CZBins/abbr_I19B2_R2.fastq | samtools view -b -S -u -F 0x0004 - > /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:01
Seeded quality full-index search: 00:32:08
# reads processed: 3000000
# reads with at least one reported alignment: 323 (0.01%)
# reads that failed to align: 2999677 (99.99%)
Reported 323 paired-end alignments to 1 output stream(s)
Time searching: 00:32:09
Overall time: 00:32:09
Beginning initialization at Mon Jan 30 13:44:11 2017...
Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:11 2017...
DONE Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:13 2017 [0:00:01.428514]...
DONE with initialization at Mon Jan 30 13:44:13 2017...
Starting iteration 0 at Mon Jan 30 13:44:13 2017...
Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:13 2017...
DONE Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:14 2017 [0:00:01.266739]...
Calculating likelihood (172, 646) for iteration 0 at Mon Jan 30 13:44:14 2017...
Calculating Pr(N=n) for iteration 0 at Mon Jan 30 13:44:14 2017...
DONE calculating Pr(N=n) for iteration 0 at Mon Jan 30 13:44:14 2017 [0:00:00.101599]...
DONE Calculating likelihood for iteration 0 at Mon Jan 30 13:44:14 2017 [0:00:00.106212]...
Calculating posteriors for iteration 0 at Mon Jan 30 13:44:14 2017...
DONE Calculating posteriors for iteration 0 at Mon Jan 30 13:44:14 2017 [0.018 seconds]...
Writing consensus for iteration 0 at Mon Jan 30 13:44:14 2017...
snp_minor_prob_thresh = 0.100
snp_percentage_thresh = 0.040
Split out 0 new minor strain sequences.
Average time for non-split sequences: [0.000007 seconds]
Culled 170 sequences
DONE Writing consensus for iteration 0 at Mon Jan 30 13:44:14 2017 [0:00:00.001942]...
Clustering sequences for iteration 0 at Mon Jan 30 13:44:14 2017...
cluster threshold = 0.970
[fai_load] build FASTA index.
[fai_load] build FASTA index.
usearch command was:
usearch -search_global /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --db /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --id 0.800 -quicksort -query_cov 0.5 -target_cov 0.5 -strand plus --userout /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta.us.txt --userfields query+target+id+caln+qlo+qhi+tlo+thi -threads 1 -fulldp
usearch v9.1.13_i86linux32, 4.0Gb RAM (65.9Gb total), 8 cores
(C) Copyright 2013-16 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch
License: czh...@jhu.edu
00:00 40Mb 100.0% Reading /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta
00:00 6.4Mb 100.0% Masking (fastnucleo)
Segmentation fault (core dumped)ter.00.cons.fasta.tmp.fasta, 0.0% matched
Traceback (most recent call last):
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 1697, in <module>
main()
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 1688, in main
do_iterations(em, max_iter = options.iterations, save_every = options.save_every)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 1439, in do_iterations
em.do_iteration(em.current_bam_filename, em.current_reference_fasta_filename)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 500, in do_iteration
self.cluster_sequences(consensus_filename) # merges sequences that have evolved to be the same (USEARCH)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 807, in cluster_sequences
return self.cluster_sequences2(fastafilename)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 871, in cluster_sequences2
check_call(cmd, shell=True, stdout = sys.stdout, stderr = sys.stderr)
File "/home/czhou.MI/miniconda2/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'usearch -search_global /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --db /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --id 0.800 -quicksort -query_cov 0.5 -target_cov 0.5 -strand plus --userout /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta.us.txt --userfields query+target+id+caln+qlo+qhi+tlo+thi -threads 1 -fulldp' returned non-zero exit status 139
Thanks,
Cyrus Z
I am a first time EMIRGE user. I am not sure what the bug is here, I was hoping you can help.
Command:
~/Desktop/CZ/EMIRGE-master/emirge.py -1 abbr_I19B2_R1.fastq -2 abbr_I19B2_R2.fastq -f ~/Desktop/CZ/EMIRGE-master/SI*fasta -b ~/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 160 -i 217 -s 53 --phred33 19B_EMIRGE_output/
Output:
imported _emirge C functions from: /home/czhou.MI/.cache/Python-Eggs/EMIRGE-0.61.0-py2.7-linux-x86_64.egg-tmp/_emirge.so
Command:
/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py -1 abbr_I19B2_R1.fastq -2 abbr_I19B2_R2.fastq -f /home/czhou.MI/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -b /home/czhou.MI/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 160 -i 217 -s 53 --phred33 19B_EMIRGE_output/
EMIRGE started at Mon Jan 30 13:12:02 2017
Performing initial mapping with command:
cat /home/czhou.MI/Desktop/CZ/CZBins/abbr_I19B2_R1.fastq | bowtie --phred33-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128 --minins 160 --maxins 376 /home/czhou.MI/Desktop/CZ/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -1 - -2 /home/czhou.MI/Desktop/CZ/CZBins/abbr_I19B2_R2.fastq | samtools view -b -S -u -F 0x0004 - > /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:01
Seeded quality full-index search: 00:32:08
# reads processed: 3000000
# reads with at least one reported alignment: 323 (0.01%)
# reads that failed to align: 2999677 (99.99%)
Reported 323 paired-end alignments to 1 output stream(s)
Time searching: 00:32:09
Overall time: 00:32:09
Beginning initialization at Mon Jan 30 13:44:11 2017...
Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:11 2017...
DONE Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:13 2017 [0:00:01.428514]...
DONE with initialization at Mon Jan 30 13:44:13 2017...
Starting iteration 0 at Mon Jan 30 13:44:13 2017...
Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:13 2017...
DONE Reading bam file /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.bam at Mon Jan 30 13:44:14 2017 [0:00:01.266739]...
Calculating likelihood (172, 646) for iteration 0 at Mon Jan 30 13:44:14 2017...
Calculating Pr(N=n) for iteration 0 at Mon Jan 30 13:44:14 2017...
DONE calculating Pr(N=n) for iteration 0 at Mon Jan 30 13:44:14 2017 [0:00:00.101599]...
DONE Calculating likelihood for iteration 0 at Mon Jan 30 13:44:14 2017 [0:00:00.106212]...
Calculating posteriors for iteration 0 at Mon Jan 30 13:44:14 2017...
DONE Calculating posteriors for iteration 0 at Mon Jan 30 13:44:14 2017 [0.018 seconds]...
Writing consensus for iteration 0 at Mon Jan 30 13:44:14 2017...
snp_minor_prob_thresh = 0.100
snp_percentage_thresh = 0.040
Split out 0 new minor strain sequences.
Average time for non-split sequences: [0.000007 seconds]
Culled 170 sequences
DONE Writing consensus for iteration 0 at Mon Jan 30 13:44:14 2017 [0:00:00.001942]...
Clustering sequences for iteration 0 at Mon Jan 30 13:44:14 2017...
cluster threshold = 0.970
[fai_load] build FASTA index.
[fai_load] build FASTA index.
usearch command was:
usearch -search_global /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --db /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --id 0.800 -quicksort -query_cov 0.5 -target_cov 0.5 -strand plus --userout /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta.us.txt --userfields query+target+id+caln+qlo+qhi+tlo+thi -threads 1 -fulldp
usearch v9.1.13_i86linux32, 4.0Gb RAM (65.9Gb total), 8 cores
(C) Copyright 2013-16 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch
License: czh...@jhu.edu
00:00 40Mb 100.0% Reading /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta
00:00 6.4Mb 100.0% Masking (fastnucleo)
Segmentation fault (core dumped)ter.00.cons.fasta.tmp.fasta, 0.0% matched
Traceback (most recent call last):
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 1697, in <module>
main()
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 1688, in main
do_iterations(em, max_iter = options.iterations, save_every = options.save_every)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 1439, in do_iterations
em.do_iteration(em.current_bam_filename, em.current_reference_fasta_filename)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 500, in do_iteration
self.cluster_sequences(consensus_filename) # merges sequences that have evolved to be the same (USEARCH)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 807, in cluster_sequences
return self.cluster_sequences2(fastafilename)
File "/home/czhou.MI/Desktop/CZ/EMIRGE-master/emirge.py", line 871, in cluster_sequences2
check_call(cmd, shell=True, stdout = sys.stdout, stderr = sys.stderr)
File "/home/czhou.MI/miniconda2/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'usearch -search_global /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --db /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta --id 0.800 -quicksort -query_cov 0.5 -target_cov 0.5 -strand plus --userout /home/czhou.MI/Desktop/CZ/CZBins/19B_EMIRGE_output/iter.00/iter.00.cons.fasta.tmp.fasta.us.txt --userfields query+target+id+caln+qlo+qhi+tlo+thi -threads 1 -fulldp' returned non-zero exit status 139
Thanks,
Cyrus Z
Ajit Kumar Patra
Feb 20, 2019, 7:04:24 PM2/20/19
to EMIRGE users
Hi Cyrus Z,
I got an error the same as yours. I hope you solved this error. Could you please tell me, how to solve this?
I got an error the same as yours. I hope you solved this error. Could you please tell me, how to solve this?
Error:
00:00 37Mb 0.1% Reading /new_project/work/ajit/Tubeworm_metagenome/EMIRGE/1368/output/iter.00/iter.00.cons.fasta.tmp.fasta^M00:00 40Mb 100.0% Reading /new_project/work/ajit/Tubeworm_metagenome/EMIRGE/1368/output/iter.00/iter.00.cons.fasta.tmp.fasta
00:00 6.5Mb 0.1% Masking (fastnucleo) ^M00:00 6.5Mb 100.0% Masking (fastnucleo)
00:00 40Mb 0.1% Searching iter.00.cons.fasta.tmp.fasta, 0.0% matched^MTraceback (most recent call last):
File "/app/redhat6/anaconda2/envs/chconda/bin/emirge.py", line 4, in <module>
__import__('pkg_resources').run_script('EMIRGE==0.61.0', 'emirge.py')
File "/app/redhat6/anaconda2/envs/chconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 657, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/app/redhat6/anaconda2/envs/chconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1444, in run_script
exec(script_code, namespace, namespace)
File "/app/redhat6/anaconda2/lib/python2.7/site-packages/EMIRGE-0.61.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/emirge.py", line 1697, in <module>
File "/app/redhat6/anaconda2/lib/python2.7/site-packages/EMIRGE-0.61.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/emirge.py", line 1688, in main
File "/app/redhat6/anaconda2/lib/python2.7/site-packages/EMIRGE-0.61.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/emirge.py", line 1439, in do_iterations
File "/app/redhat6/anaconda2/lib/python2.7/site-packages/EMIRGE-0.61.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/emirge.py", line 500, in do_iteration
File "/app/redhat6/anaconda2/lib/python2.7/site-packages/EMIRGE-0.61.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/emirge.py", line 807, in cluster_sequences
File "/app/redhat6/anaconda2/lib/python2.7/site-packages/EMIRGE-0.61.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/emirge.py", line 871, in cluster_sequences2
File "/app/redhat6/anaconda2/envs/chconda/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'usearch -search_global /new_project/work/ajit/Tubeworm_metagenome/EMIRGE/1368/output/iter.00/iter.00.cons.fasta.tmp.fasta --db /new_project/work/ajit/Tubeworm_metagenome/EMIRGE/1368/output/iter.00/iter.00.cons.fasta.tmp.fasta --id 0.800 -quicksort -query_cov 0.5 -target_cov 0.5 -strand plus --userout /new_project/work/ajit/Tubeworm_metagenome/EMIRGE/1368/output/iter.00/iter.00.cons.fasta.tmp.fasta.us.txt --userfields query+target+id+caln+qlo+qhi+tlo+thi -threads 6 -fulldp' returned non-zero exit status -11
Command exited with non-zero status 1
Command being timed: "emirge.py /new_project/work/ajit/Tubeworm_metagenome/EMIRGE/1368/output -1 1368_1.fastq -2 1368_2.fastq -f /new_project/work/ajit/Tubeworm_metagenome/SILVA_132_SSURef/SILVA_132_SSURef_tax_silva.fasta -b /new_project/work/ajit/Tubeworm_metagenome/SILVA_132_SSURef/SILVA_132_SSURef -l 100 -a 16 -i 168 -s 161"
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