problem in emirge

[debji...@gmail.com]

Hi,

I get an error by running the emirge.py program, please help me out to solve this problem. Below the snapshot of the error,

debjit@debjit-HP-406-G1-MT[EMIRGE-master] python emirge.py ./ -1 SRR1910843.sra.fastq -f SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -b SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 350

If you use EMIRGE in your work, please cite these manuscripts, as appropriate.

Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF (2011)

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.

Genome biology 12: R44. doi:10.1186/gb-2011-12-5-r44.

Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF (2013)

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments.

PloS one 8: e56018. doi:10.1371/journal.pone.0056018.

imported _emirge C functions from: /home/debjit/.python-eggs/EMIRGE-0.61.0-py2.7-linux-x86_64.egg-tmp/_emirge.so

Command:

emirge.py ./ -1 SRR1910843.sra.fastq -f SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -b SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 350

EMIRGE started at Wed Jul  5 17:14:46 2017

Performing initial mapping with command:

cat  /home/debjit/EMIRGE-master/SRR1910843.sra.fastq |  bowtie --phred64-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128  /home/debjit/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed - | samtools view -b -S -u -F 0x0004 - > /home/debjit/EMIRGE-master/initial_mapping/initial_bowtie_mapping.PE.bam 

Time loading forward index: 00:00:00

Time loading mirror index: 00:00:01

Saw ASCII character 33 but expected 64-based Phred qual.

Try not specifying --solexa1.3-quals/--phred64-quals.

terminate called after throwing an instance of 'int'

Aborted

cat: write error: Broken pipe

[samopen] SAM header is present: 188937 sequences.

[sam_read1] reference 'ID:Bowtie VN:1.1.1 CL:"bowtie --wrapper basic-0 --phred64-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128 /home/debjit/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -"

12.1.2000 LN:2000

@SQ SN:GU556149.1.2000 LN:2000

!' is recognized as '*'.

[main_samview] truncated file.

Traceback (most recent call last):

  File "emirge.py", line 1697, in <module>

    main()

  File "emirge.py", line 1659, in main

    options.mapping = do_initial_mapping(working_dir, options)

  File "emirge.py", line 1486, in do_initial_mapping

    check_call(cmd, shell=True, stdout = sys.stdout, stderr = sys.stderr)

  File "/usr/lib/python2.7/subprocess.py", line 540, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'cat  /home/debjit/EMIRGE-master/SRR1910843.sra.fastq |  bowtie --phred64-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128  /home/debjit/EMIRGE-master/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed - | samtools view -b -S -u -F 0x0004 - > /home/debjit/EMIRGE-master/initial_mapping/initial_bowtie_mapping.PE.bam ' returned non-zero exit status 1

Thank You,

Debjit De

[Chris Miller]

Debjit, 

It looks like you need to specify that you have 33-based quality encoding.  Try adding 

  --phred33

to your command line. 

Chris 

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