MaSuRCA 3.2.6: failed to merge alignments

[TimothyStephens]

Hi,

Sorry for posting so many issues. I am running MaSuRCA 3.2.6 and I get the below error.

[Fri Aug 31 14:49:21 AEST 2018] Processing pe library reads [Fri Aug 31 14:49:21 AEST 2018] Processing sj library reads [Fri Aug 31 14:49:22 AEST 2018] Average PE read length 150 [Fri Aug 31 14:49:23 AEST 2018] Using kmer size of 99 for the graph cat: write error: Broken pipe [Fri Aug 31 14:49:23 AEST 2018] MIN_Q_CHAR: 33 [Fri Aug 31 14:49:23 AEST 2018] Estimated genome size: 2238525004 [Fri Aug 31 14:49:23 AEST 2018] Computing super reads from PE Using CABOG from is /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin Running mega-reads correction/assembly Using mer size 15 for mapping, B=17, d=0.029 Estimated Genome Size 2238525004 Estimated Ploidy 2 Using 24 threads Output prefix mr.41.15.17.0.029

gzip: stdout: Broken pipe Pacbio coverage <44x, using the longest subreads Refining alignments ERROR: failed to merge alignments at position 969 Please file a bug report ERROR: Could not parse delta file, /dev/stdin error no: 402 ERROR: Could not parse delta file, /dev/stdin error no: 402 Joining Generating assembly input files Coverage threshold for splitting unitigs is 28 minimum ovl 63 Running assembly

I have done a test install (as suggested in issue #4 ) and cant find an issue. The job was given 4Tb of memory (it only used 940Gb) so I don’t think its a problem with too little memory (as suggested in #37 ).

Thanks, Tim.

[alekseyzimin]

This is not a big deal, you can just continue. This error will have very minimal to none impact on assembly quality.

[TimothyStephens]

Thank You!

[khaled8523]

I have same problem but at the end Masurca is not able to do the assembly. I have enclosed the Slurm output and configuration file. I appreciate you if you could give me hint to solve this problem.