AriocP later than AriocP v1.50.3040.21310 (release) +2021-11-06T22:04:41 segfaults when run in Docker

[karlkashofer]

Dear Richard ! I run AriocP in a docker container. This seems to be broken in releases after 2021-11-06. Releases after that produce a segfault and coredump immediately after loading the LUTs.

docker run -it --gpus all -v /scratch:/scratch -v $PWD:/analysis fc918299b19f bash -c "cd /scratch/tmp; AriocP /analysis/ariocP.1054455"
=> NOT working
docker run --gpus all -v /scratch:/scratch -v $PWD:/analysis d0a059138d42 bash -c "cd /scratch/tmp; AriocP /analysis/ariocP.1054455"
=> working

<none>                                                                          <none>               dde502acd4df   7 weeks ago     5.85GB NOT working
<none>                                                                          <none>               fc918299b19f   7 weeks ago     5.85GB NOT working
<none>                                                                          <none>               d0a059138d42   7 weeks ago     5.85GB working
<none>                                                                          <none>               de703eee3b01   7 weeks ago     5.85GB working

devarea@sx253:~/2021-10_NovaSeq_Pipelines/Analysis/A274_16$ for i in fc918299b19f d0a059138d42; do docker run -v $PWD:/analysis $i bash -c "/bin/AriocP";done
150704980 [00000001] AriocP v1.50.3053.21328 (release) +2021-11-24T11:46:19
150704986 [00000001] Copyright (c) 2015-2021 Johns Hopkins University.  All rights reserved.
150704986 [00000001]  compiled             : 2021-11-25T11:20:16 (GNU g++ v10.2.1)
150704986 [00000001]  data type sizes      : int=4 long=8 *=8 Jvalue5=5 Jvalue8=8 JtableHeader=5 (little-endian)
150704986 [00000001]  computer name        : 63d58b0d2f78
150704986 [00000001]  operating system     : Debian GNU/Linux 11 (bullseye)
150704986 [00000001]  executable file      : /bin/AriocP
150704988 [00000001] ApplicationException ([0x00000001] AriocCommon/AppGlobalCommon.cpp 175): cannot open configuration file './AriocP.cfg'
150704988 [00000001] AriocP ends (1)
150705893 [00000001] AriocP v1.50.3040.21310 (release) +2021-11-06T22:04:41
150705896 [00000001] Copyright (c) 2015-2021 Johns Hopkins University.  All rights reserved.
150705896 [00000001]  compiled             : 2021-11-13T12:33:01 (GNU g++ v10.2.1)
150705896 [00000001]  data type sizes      : int=4 long=8 *=8 Jvalue5=5 Jvalue8=8 JtableHeader=5 (little-endian)
150705896 [00000001]  computer name        : be8375a0bdce
150705896 [00000001]  operating system     : Debian GNU/Linux 11 (bullseye)
150705896 [00000001]  executable file      : /bin/AriocP
150705897 [00000001] ApplicationException ([0x00000001] AriocCommon/AppGlobalCommon.cpp 175): cannot open configuration file './AriocP.cfg'
150705897 [00000001] AriocP ends (1)

Any idea what to do ? Do you know what changed ? Cheers, KK

[RWilton]

The error message claims that AriocP cannot open the configuration file at ./AriocP.cfg. This error appears when AriocP does not find a configuration file specification on the command line and then tries to open a default configuration file in the current working directory,

My approach to troubleshooting this would be simply to invoke AriocP interactively from within a shell executing inside the Docker container. If you can verify that the configuration file is indeed where it's expected to be (e.g., by executing cat /path/to/AriocP.cfg) then it should be clear whether the problem lies with the command line file specification or with some anomaly within AriocP's file-open implementation.

[karlkashofer]

OK, it was my mistake. The SAMtags feature we built for Agilent XT libraries <dataIn sequenceType="Q" QNAME="(*)\t*" SAMtags="*\t(*)"> leads to corrupt data when there are not tabs in the fastq names. I need to do separate encoding setups for normal fastqs and Agilent XT preprocessed fastqs.

Sorry for the false alarm, cheers, KK