CA failed

[EglantineMB]

Hi,

thank you so much for developping such a great assembler! I am trying to run my first assembly, I have only pool-sequencing data paired-end illumina read and I want to generate a draft assembly from that to assess a specific part of the genome later on.

However, whatever I run masurca in slurm or in an interactive session on a node I always encounter an issue at CA step that stop the assembly. Here is the line in runCA1.out where the error is mentionned:

runCA failed.

---

Stack trace:

at /scicore/soft/apps/MaSuRCA/4.0.9-foss-2021a-Perl-5.32.1/bin/../bin/runCA line 1613, line 198.
main::caFailure("ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1"..., undef) called at /scicore/soft/apps/MaSuRCA/4.0.9-foss-2021a-Perl-5.32.1/bin/../bin/runCA line 3863
main::checkOverlapper("normal") called at /scicore/soft/apps/MaSuRCA/4.0.9-foss-2021a-Perl-5.32.1/bin/../bin/runCA line 3914
main::checkOverlap("normal") called at /scicore/soft/apps/MaSuRCA/4.0.9-foss-2021a-Perl-5.32.1/bin/../bin/runCA line 6526

---

Failure message:

ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000001 FAILED.
ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000002 FAILED.
ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000003 FAILED.
ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000004 FAILED.
ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000005 FAILED.
ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000006 FAILED.
ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000007 FAILED.
ERROR: Overlap job /scicore/home/ebertd/mathie0002/PoolSeq/1_assembly_S/CA/1-overlapper/001/000008 FAILED
etc

My command is the following one: masurca -t 32 -i ../0_Data/TNRA21Srep1_R1.fastq.gz ../0_Data/TNRA21Srep1_R2.fastq.gz