Pbjelly in pbsuite 14.1.15: m4pie.py at mapping stage error

[giancarlo russo]

Hi Adam, I keep having the same problem as I had with versions 13 and 14.1.14: the setup goes fine but then the filtered_subreads.fastq.err files reads:

2014-02-01 18:43:24,154 [INFO] Running /usr/local/ngseq/src/PBSuite_14.1.15/bin/m4pie.py /usr/local/ngseq/src/PBSuite_14.1.15/docs/jellyExample/mapping/filtered_subreads.fastq.m4 /u
sr/local/ngseq/src/PBSuite_14.1.15/docs/jellyExample/data/reads/filtered_subreads.fastq /usr/local/ngseq/src/PBSuite_14.1.15/docs/jellyExample/data/reference/lambda.fasta --nproc 4
-i
Traceback (most recent call last):
File "/usr/local/ngseq/src/PBSuite_14.1.15/bin/m4pie.py", line 203, in <module>
run(sys.argv[1:])
File "/usr/local/ngseq/src/PBSuite_14.1.15/bin/m4pie.py", line 165, in run
aligns = M4File(args.m4)
File "/usr/local/ngseq/src/PBSuite_14.1.15/pbsuite/utils/FileHandlers.py", line 473, in init
file = open(file,'r')
IOError: [Errno 2] No such file or directory: '/usr/local/ngseq/src/PBSuite_14.1.15/docs/jellyExample/mapping/filtered_subreads.fastq.m4'

as if a .m4 files is needed. Again, this happens with the example files.
Any ideas?

Thanks,
G

[Adam English]

Another user with a similar problem was able to correct the issue by ensuring blasr and sawriter were in his $PATH.

[Jonas Söderberg]

I have the same problem, but both blasr and sawriter are in my $PATH. I have this very similar output:

2014-07-31 17:02:39,157 [INFO] Running /opt/sw/PBSuite/14.6.24/bin/m4pie.py /proj/micro-nitens/analysis/PBdata/output/mapping/pb_52_filtered_subreads.fastq.m4 /proj/micro-nitens/PacBio/filtered_reads/pb_52_filtered_subreads.fastq /proj/micro-nitens/analysis/PBdata/reference/454ScaffoldContigs.fasta --nproc 8 -i
Traceback (most recent call last):
  File "/opt/sw/PBSuite/14.6.24/bin/m4pie.py", line 206, in <module>
    run(sys.argv[1:])
  File "/opt/sw/PBSuite/14.6.24/bin/m4pie.py", line 168, in run
    aligns = M4File(args.m4)
  File "/opt/sw/PBSuite/14.6.24/pbsuite/utils/FileHandlers.py", line 484, in __init__
    file = open(file,'r')
IOError: [Errno 2] No such file or directory: '/proj/micro-nitens/analysis/PBdata/output/mapping/pb_52_filtered_subreads.fastq.m4'

PBjelly just seems to skip that part, blasr I guess, but I can run blasr fine when doing it myself, e.g. the following works:

module load PBSuite; blasr /proj/micro-nitens/PacBio/filtered_reads/pb_52_filtered_subreads.fastq /proj/micro-nitens/analysis/PBdata/reference/454ScaffoldContigs.fasta -minMatch 8 -minPctIdentity 70 -bestn 8 -nCandidates 30 -maxScore -500 -nproc 8 -noSplitSubreads -out test

This, however, fails:

module load PBSuite; Jelly.py support Protocol.xml

Protocol.xml:

<jellyProtocol>
<reference>/proj/micro-nitens/analysis/PBdata/reference/454ScaffoldContigs.fasta</reference>
<outputDir>/proj/micro-nitens/analysis/PBdata/output/</outputDir>
<blasr>-minMatch 8 -minPctIdentity 70 -bestn 8 -nCandidates 30 -maxScore -500 -nproc 8 -noSplitSubreads</blasr>
<input baseDir="/proj/micro-nitens/PacBio/filtered_reads/">
<job>pb_52_filtered_subreads.fastq</job>
</input>
</jellyProtocol>