EMIRGE error - too few reads?

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Lizzy Wilbanks

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Jul 20, 2016, 4:51:37 PM7/20/16

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Hi Chris,

I was having a whirl at running EMIRGE on a relatively low coverage surface ocean dataset. I'm wondering if this error I got is due to there just not being enough data to run it, or perhaps something fixable?

Thanks!

Lizzy

\~> emirge.py /export/data1/projects/wilbanks/plumes_blumes/emirge/ \

> -b /export/data1/db/emirge/default/SSURef_111_candidate_db \

> -l 300 -i 50 -s 250 --phred33 -a 16 \

> -1 /export/data1/projects/wilbanks/plumes_blumes/trimmed_fastq_q10/PnB-0212-4S-mg_S1_L001_R1_pe.fastq \

> -2 /export/data1/projects/wilbanks/plumes_blumes/trimmed_fastq_q10/PnB-0212-4S-mg_S1_L001_R2_pe.fastq

imported _emirge C functions from: /export/data1/sw/emirge/0.60/lib/python2.7/site-packages/_emirge.so

Command:

/export/data1/sw/emirge/0.60/bin/emirge.py /export/data1/projects/wilbanks/plumes_blumes/emirge/ -b /export/data1/db/emirge/default/SSURef_111_candidate_db -l 300 -i 50 -s 250 --phred33 -a 16 -1 /export/data1/projects/wilbanks/plumes_blumes/trimmed_fastq_q10/PnB-0212-4S-mg_S1_L001_R1_pe.fastq -2 /export/data1/projects/wilbanks/plumes_blumes/trimmed_fastq_q10/PnB-0212-4S-mg_S1_L001_R2_pe.fastq

Performing initial mapping with command:

cat /export/data1/projects/wilbanks/plumes_blumes/trimmed_fastq_q10/PnB-0212-4S-mg_S1_L001_R1_pe.fastq | bowtie --phred33-quals -t -p 16 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128 --minins 300 --maxins 800 /export/data1/db/emirge/default/SSURef_111_candidate_db -1 - -2 /export/data1/projects/wilbanks/plumes_blumes/trimmed_fastq_q10/PnB-0212-4S-mg_S1_L001_R2_pe.fastq | samtools view -b -S -u -F 0x0004 - -o /export/data1/projects/wilbanks/plumes_blumes/emirge/initial_mapping/initial_bowtie_mapping.PE.bam

Time loading reference: 00:00:01

Time loading forward index: 00:00:01

Time loading mirror index: 00:00:00

Seeded quality full-index search: 00:02:36

# reads processed: 766698

# reads with at least one reported alignment: 283 (0.04%)

# reads that failed to align: 766415 (99.96%)

Reported 283 paired-end alignments to 1 output stream(s)

Time searching: 00:02:40

Overall time: 00:02:40

Beginning initialization at Wed Jul 20 12:18:56 2016...

Reading bam file /export/data1/projects/wilbanks/plumes_blumes/emirge/initial_mapping/initial_bowtie_mapping.PE.bam at Wed Jul 20 12:18:56 2016...

Traceback (most recent call last):

File "/export/data1/sw/emirge/0.60/bin/emirge.py", line 1615, in <module>

main()

File "/export/data1/sw/emirge/0.60/bin/emirge.py", line 1605, in main

em.initialize_EM(options.mapping, options.fasta_db)

File "/export/data1/sw/emirge/0.60/bin/emirge.py", line 329, in initialize_EM

self.read_bam(bam_filename, reference_fasta_filename)

File "/export/data1/sw/emirge/0.60/bin/emirge.py", line 214, in read_bam

self.fastafile = pysam.Fastafile(self.current_reference_fasta_filename)

File "pysam/cfaidx.pyx", line 81, in pysam.cfaidx.FastaFile.__cinit__ (pysam/cfaidx.c:1675)

File "pysam/cfaidx.pyx", line 102, in pysam.cfaidx.FastaFile._open (pysam/cfaidx.c:2224)