ERROR: Failed with signal HUP (1)

Question

[pqgood]

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START Wed Apr 29 14:22:08 2015
mkdir tempS3
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END Wed Apr 29 14:22:08 2015 (0 seconds)
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START Wed Apr 29 14:22:08 2015
/NABIC/HOME/jsnkim/shinig/soft/wgs-8.3rc1/Linux-amd64/bin/fastqToCA -libraryname S3 -type sanger -technology none -feature doConsensusCorrection 1 -reads /NABIC/HOME/jsnkim/shinig/test/sampleData/pacbio.filtered_subreads.fasta > /NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.frg
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END Wed Apr 29 14:22:08 2015 (0 seconds)
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START Wed Apr 29 14:22:08 2015
/NABIC/HOME/jsnkim/shinig/soft/wgs-8.3rc1/Linux-amd64/bin/runCA  -s /NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.spec -p asm -d tempS3  stopAfter=initialStoreBuilding  /NABIC/HOME/jsnkim/shinig/test/sampleData/illumina.frg /NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.frg
----------------------------------------
START Wed Apr 29 14:22:08 2015
/NABIC/HOME/jsnkim/shinig/soft/wgs-8.3rc1/Linux-amd64/bin/gatekeeper  -o /NABIC/HOME/jsnkim/shinig/test/sampleData/tempS3/asm.gkpStore.BUILDING  -F  /NABIC/HOME/jsnkim/shinig/test/sampleData/illumina.frg /NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.frg > /NABIC/HOME/jsnkim/shinig/test/sampleData/tempS3/asm.gkpStore.err 2>&1
----------------------------------------
END Wed Apr 29 14:22:15 2015 (7 seconds)
ERROR: Failed with signal HUP (1)
runCA failed.

----------------------------------------
Stack trace:

 at /NABIC/HOME/jsnkim/shinig/soft/wgs-8.3rc1/Linux-amd64/bin/runCA line 1649.
    main::caFailure("gatekeeper failed", "/NABIC/HOME/jsnkim/shinig/test/sampleData/tempS3/asm.gkpStore"...) called at /NABIC/HOME/jsnkim/shinig/soft/wgs-8.3rc1/Linux-amd64/bin/runCA line 1978
    main::preoverlap("/NABIC/HOME/jsnkim/shinig/test/sampleData/illumina.frg", "/NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.frg") called at /NABIC/HOME/jsnkim/shinig/soft/wgs-8.3rc1/Linux-amd64/bin/runCA line 6551

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Last few lines of the relevant log file (/NABIC/HOME/jsnkim/shinig/test/sampleData/tempS3/asm.gkpStore.err):


Starting file '/NABIC/HOME/jsnkim/shinig/test/sampleData/illumina.frg'.

Processing SINGLE-ENDED SANGER QV encoding reads from:
      '/NABIC/HOME/jsnkim/shinig/test/sampleData/illumina.fastq'

Starting file '/NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.frg'.

Processing SINGLE-ENDED SANGER QV encoding reads from:
      '/NABIC/HOME/jsnkim/shinig/test/sampleData/pacbio.filtered_subreads.fasta'


GKP finished with 3775 alerts or errors:
3775    # ILL Error: not a sequence start line.

ERROR: library IID 2 'S3' has inf% errors or warnings.

----------------------------------------
Failure message:

gatekeeper failed

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END Wed Apr 29 14:22:15 2015 (7 seconds)
Failed to execute /NABIC/HOME/jsnkim/shinig/soft/wgs-8.3rc1/Linux-amd64/bin/runCA  -s /NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.spec -p asm -d tempS3  stopAfter=initialStoreBuilding  /NABIC/HOME/jsnkim/shinig/test/sampleData/illumina.frg /NABIC/HOME/jsnkim/shinig/test/sampleData//tempS3/S3.frg
[jsnkim@NGS sampleData]$

[Jean-Karim Heriche]

Did you read this line: # ILL Error: not a sequence start line.?

Could it be that your input file is badly formatted?

Error messages and logs normally contain information even if sometimes cryptic so spend time trying to understand them.

'signal HUP' suggests that your process was terminated with a SIGHUP signal which usually means the process has lost connection with its controlling terminal or a server.

[PoGibas]

And your question is ... ?

[pqgood]

I don't know

ERROR: Failed with signal HUP(1) Error

What is ERROR: Failed with signal HUP(1)?

[Sheetal]

Could somebody help me in finding out the error in masurca assembly

CA failed, check output under CA/ and runCA3.out

runCA03.out file content:

----------------------------------------
START Tue Sep 24 02:38:39 2019
/opt/MaSuRCA-3.3.3/CA8/Linux-amd64/bin/cgw  \
  -j 1 -k 5 \
  -r 5 \
  -s 2 \
  -filter 1 \
  -minmergeweight 2 \
  -P 2 \
  -B 1402351 \
  -shatter 0 \
  -missingMate 0 \
  -m 100 \
  -g /fabsnew2-commondbs/sheetal/data_analysis/masurca_output/CA/genome.gkpStore \
  -t /fabsnew2-commondbs/sheetal/data_analysis/masurca_output/CA/genome.tigStore \
  -o /fabsnew2-commondbs/sheetal/data_analysis/masurca_output/CA/7-0-CGW/genome \
 > /fabsnew2-commondbs/sheetal/data_analysis/masurca_output/CA/7-0-CGW/cgw.out 2>&1
----------------------------------------
END Tue Sep 24 17:11:20 2019 (52361 seconds)

ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at /opt/MaSuRCA-3.3.3/bin/../CA8/Linux-amd64/bin/runCA line 1613.
        main::caFailure('scaffolder failed', '/fabsnew2-commondbs/sheetal/data_analysis/masurca_output/CA/7...') called at /opt/MaSuRCA-3.3.3/bin/../CA8/Linux-amd64/bin/runCA line 5309
        main::CGW('7-0-CGW', undef, '/fabsnew2-commondbs/sheetal/data_analysis/masurca_output/CA/g...', 2, undef, 1) called at /opt/MaSuRCA-3.3.3/bin/../CA8/Linux-amd64/bin/runCA line 5528
        main::scaffolder() called at /opt/MaSuRCA-3.3.3/bin/../CA8/Linux-amd64/bin/runCA line 6530

----------------------------------------
Last few lines of the relevant log file (/fabsnew2-commondbs/sheetal/data_analysis/masurca_output/CA/7-0-CGW/cgw.out):

CreateAContigInScaffold()-- contig 73415904 (original 73415904)  1747-5023

* CIScaffold 4141141 numCI:4 (a:73415903 b:4960226)  length: 7847
> Includes CIs
             0: CI 73415903 sid  4141141 len    1992,     51.8 ends       0,   1992 var       0.0,     51.8 orient F
             1: CI 73415904 sid  4141141 len    3276,     85.2 ends    1747,   5023 var    3191.3,   3276.4 orient F
             2: CI 65039086 sid  4141141 len    2167,     56.3 ends    5079,   7246 var    7442.5,   7498.9 orient F
             3: CI  4960226 sid  4141141 len     594,     15.4 ends    7847,   7253 var   10665.2,  10649.8 orient R
>  M  Edges A 
>  M  Edges B
CreateAContigInScaffold()-- new contig 73416203 in scaffold 4141166
CreateAContigInScaffold()-- new contig 73416204 in scaffold 4141220
MergeMultiAlignsFast_new()-- failed to find overlap between contigs 73415909 and 65484736.
CreateAContigInScaffold()-- MergeMultiAlignsFast_new() failed.
CreateAContigInScaffold()-- contig 73415909 (original 73415909)  0-4421
CreateAContigInScaffold()-- contig 65484736 (original 65484736)  4933-4286

* CIScaffold 4141417 numCI:2 (a:73415909 b:65484736)  length: 4933
> Includes CIs
             0: CI 73415909 sid  4141417 len    4421,    114.9 ends       0,   4421 var       0.0,    114.9 orient F
             1: CI 65484736 sid  4141417 len     647,     16.8 ends    4933,   4286 var    2364.2,   2347.4 orient R
>  M  Edges A 
>  M  Edges B
MergeMultiAlignsFast_new()-- failed to find overlap between contigs 73415912 and 73415913.
CreateAContigInScaffold()-- MergeMultiAlignsFast_new() failed.
CreateAContigInScaffold()-- contig 73415912 (original 73415912)  0-622
CreateAContigInScaffold()-- contig 73415913 (original 73415913)  435-1684

* CIScaffold 4141424 numCI:2 (a:73415912 b:73415913)  length: 1684
> Includes CIs
             0: CI 73415912 sid  4141424 len     622,     16.2 ends       0,    622 var       0.0,     16.2 orient F
             1: CI 73415913 sid  4141424 len    1249,     32.5 ends     435,   1684 var    6320.4,   6352.9 orient F
>  M  Edges A 
>  M  Edges B
CreateAContigInScaffold()-- new contig 73416205 in scaffold 4141467
CreateAContigInScaffold()-- new contig 73416206 in scaffold 4141537
CreateAContigInScaffold()-- new contig 73416207 in scaffold 4141736
CreateAContigInScaffold()-- new contig 73416208 in scaffold 4141776
CreateAContigInScaffold()-- new contig 73416209 in scaffold 4141798
SetCIScaffoldTLength()-- adjusted scaffold 4141798 from (2345 +- 3696) to (1396 +- 36)
CreateAContigInScaffold()-- new contig 73416210 in scaffold 4141856
CreateAContigInScaffold()-- n

Answer 1

[Medhat]

That means you have problem in the input files so the process terminated. try to revisit how did you do your .frg file