Pysam stats failure

[BenjaminSSimpson]

I have been trying to get the program up and running over the last couple of days. I am using a HPC that uses SLURM and a linux-style interface. I have used the instructions on the Install-and-Run.md sheet, following all the options for users without root privileges.

When running example file 1, I simply receive the error message: "Pysamstats failure". I checked the logs but for sample1.failed it just repeats this message. I opened python to check that it could successfully import Pysamstats, and it can. The python path is added to the run.sh file as suggested. I tried re-installing pysamstats but this did not do anything.

It is a tad difficult to troubleshoot this error, do you have any suggestions?

Best wishes,

Ben

[jsicherman]

Reviving this because I have the same issue. Relevant part of the errorlog from example2, s2.log...

htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: ./align/s2.extendedFrags.bam (No such file or directory)
        at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:714)
        at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:189)
        at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:144)
        at abra.Sam2Fastq.convert(Sam2Fastq.java:49)
        at abra.ReAligner.sam2Fastq(ReAligner.java:803)
        at abra.PreprocessReadsRunnable.go(PreprocessReadsRunnable.java:32)
        at abra.AbraRunnable.run(AbraRunnable.java:20)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.io.FileNotFoundException: ./align/s2.extendedFrags.bam (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:674)
Loading reference map:  ./align/amp.fa
        ... 11 more
        Chromosome: amplicon length: 738
Done loading ref map.  Elapsed secs: 0
Tue Jan 25 12:50:57 PST 2022 : Reading Input SAM Header and identifying read length
Tue Jan 25 12:50:57 PST 2022 : Identifying header and determining read length
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: ./align/s2.notCombined.bam (No such file or directory)
        at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:714)
        at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:189)
        at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:144)
        at abra.ReAligner.getSamHeaderAndReadLength(ReAligner.java:734)
        at abra.ReAligner.reAlign(ReAligner.java:127)
        at abra.ReAligner.run(ReAligner.java:1240)
        at abra.Abra.main(Abra.java:12)
Caused by: java.io.FileNotFoundException: ./align/s2.notCombined.bam (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:674)
        ... 6 more
Traceback (most recent call last):
  File "/home/jordan/bin/pysamstats", line 231, in <module>
    fields=fields,
  File "pysamstats.pyx", line 3894, in pysamstats.write_csv (pysamstats.c:38227)
  File "pysamstats.pyx", line 891, in pysamstats.stat_variation (pysamstats.c:11459)
  File "pysamstats.pyx", line 3649, in pysamstats._iter_pileup (pysamstats.c:33802)
  File "pysam/calignmentfile.pyx", line 318, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4730)
  File "pysam/calignmentfile.pyx", line 403, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:5841)
  File "pysam/calignmentfile.pyx", line 574, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:7746)
ValueError: file header is empty (mode='r') - is it SAM/BAM format?