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HenrikBengtsson / CostelloPSCNSeq

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data
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TROUBLESHOOT: 3.pcsbs.R #9

Closed HenrikBengtsson closed 7 years ago

HenrikBengtsson commented 7 years ago

Running qcmd --exec Rscript 3.pscbs.R with chromosomes: c(1:22, "X", "Y", "M") gave:

[...]
Sample 1 ('Patient300,Z00363_vs_Z00346') of 1 ...
...
Loading required package: methods

Attaching package: 'methods'

The following objects are masked from 'package:R.oo':

    getClasses, getMethods

Sample 1 ('Patient300,Z00363_vs_Z00346') of 1 ...
...done
Error: Log file for job with id 1 not available
Execution halted
Warning message:
In delete.BatchtoolsFuture(future, onRunning = "skip", onMissing = "ignore",  :
  Will not remove batchtools registry, because the status of the batchtools was 'defined', 'error', 'running', 'started', 'submitted', 'system' and option 'future.del\
ete' is FALSE or running in an interactive session: '/home/henrik/projects/CostelloJ-PSCN-Seq_tests/.future/20170625_234757-0ss9xx/sample_1_1462898678'

Action

  1. Check if it can be replicated.
  2. If so, troubleshoot and fix bug.
HenrikBengtsson commented 7 years ago

Tracing the error message:

$ tail /home/henrik/projects/CostelloJ-PSCN-Seq_tests/.future/20170625_234757-0ss9xx/sample_1_1462898678/logs/job8fb8e4ac419def065d6b7b6427386fda.log
  Sample 'Patient300,Z00363_vs_Z00346'; Chromosome 24
 Chromosome #25 ('24') of 25...done
Paired PSCBS on SeqzFileSet...done
Error : BatchtoolsError in BatchtoolsFuture ('chr=1-Patient300,Z00363_vs_Z00346'): 'Error in file(pathname, open = "r") : cannot open the connection'

### [bt 2017-06-25 23:52:30]: Job terminated with an exception [batchtools job.id=1]
### [bt 2017-06-25 23:52:30]: Calculation finished!
Warning message:
In delete.BatchtoolsFuture(future, onRunning = "skip", onMissing = "ignore",  :
  Will not remove batchtools registry, because the status of the batchtools was 'defined', 'error', 'started', 'submitted' and option 'future.delete' is FALSE or running in an interactive session: '/home/henrik/projects/CostelloJ-PSCN-Seq_tests/.future/20170625_234903-kKwVia/chr1-Patient300Z00363_vs_Z00346_1452314220'

which leads to

$ tail -8 /home/henrik/projects/CostelloJ-PSCN-Seq_tests/.future/20170625_234903-kKwVia/chr1-Patient300Z00363_vs_Z00346_1452314220/logs/job88a7ddc0d8a9ff087e260b10e37c2046.log 

### [bt 2017-06-25 23:50:08]: Starting job [batchtools job.id=1]
20170625 23:50:08|Reading seqz data...
Warning in file(pathname, open = "r") :
  cannot open file 'seqzData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal,seqz/Homo_sapiens/Patient300,Z00363_vs_Z00346,chr=chr1.seqz': No such file or directory
Error in file(pathname, open = "r") : cannot open the connection

### [bt 2017-06-25 23:50:09]: Job terminated with an exception [batchtools job.id=1]
### [bt 2017-06-25 23:50:09]: Calculation finished!

In other words, when the job processing Chr 1 started, it was looking for file seqzData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal,seqz/Homo_sapiens/Patient300,Z00363_vs_Z00346,chr=chr1.seqz but failed to locate it.

Now, that's weird, because it should be looking for the gzip'ed *.seqz.gz file. I'll inspect further.

HenrikBengtsson commented 7 years ago

I cannot reproduce this; and I don't have a good idea why it happened. I'll close, but at least we have a record of it showing it may happen.