error when run manta

[ytguojian]

Hi,
According to the Manta User Guide, I tried to run manta using the following commands ---"/workspace/hrajxg/software/manta-1.3.0.centos6_x86_64/bin/configManta.py --bam /workspace/hrajxg/bioinf_Prunus_ZFRI/03_samtools/creat_sort_bam/1001.sorted.bam --referenceFasta /workspace/hrajxg/bioinf_Prunus_ZFRI/reference/Prunus_persica_v2.0.a1_scaffolds.fasta --runDir /workspace/hrajxg/bioinf_Prunus_ZFRI/010_manta" and "/workspace/hrajxg/bioinf_Prunus_ZFRI/010_manta/runWorkflow.py -m local -j 8 --quiet"

The error message is like this:
File "/workspace/hrajxg/bioinf_Prunus_ZFRI/010_manta/runWorkflow.py", line 179, in
main(r"/workspace/hrajxg/bioinf_Prunus_ZFRI/010_manta/runWorkflow.py.config.pickle","manta",MantaWorkflow)
File "/workspace/hrajxg/bioinf_Prunus_ZFRI/010_manta/runWorkflow.py", line 171, in main
errorLogFile=errorpath)
File "/workspace/hrajxg/software/manta-1.3.0.centos6_x86_64/lib/python/pyflow/pyflow.py", line 3463, in run
self._killWorkflow(msg)
File "/workspace/hrajxg/software/manta-1.3.0.centos6_x86_64/lib/python/pyflow/pyflow.py", line 4189, in _killWorkflow
self._shutdownAll(timeoutSec=10)
File "/workspace/hrajxg/software/manta-1.3.0.centos6_x86_64/lib/python/pyflow/pyflow.py", line 4202, in _shutdownAll
time.sleep(1)

Could you help me?
cheers,
Jian

[ctsa]

Hi Jian, Thanks for reporting an issue. I wonder, is the above segment of log output complete? Would it be possible for you to run through this sequence again but (1) take off the --quite option and (2) include as much of the resulting log output as practical?

[ytguojian]

Hi Chris,
Yes, it succeed when I take off the --quite option and delete all the temp files. Thanks for your response.
Here I have another question. Could I run multiple samples up to 357 with this protocol? I have run it for a few hours. It is still running. If there are problems, I will let you know.
Cheers,
Jian

[ctsa]

We support and test joint calling at 'family-scale' (roughly 10 or fewer samples). Joint analysis of 357 samples is unlikely to be successful. You might consider running the samples individually in manta and then use the recently released paragraph tool (https://github.com/Illumina/paragraph) for merging and joint genotyping.

[ytguojian]

Yes, you are right. 357 samples are too many to joint analysis. Thanks for your suggestions.