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morispi / CONSENT

Scalable long read self-correction and assembly polishing with multiple sequence alignment
https://doi.org/10.1038/s41598-020-80757-5
GNU Affero General Public License v3.0
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Illegal Instruction in CONSENT-polish #29

Open Maggi-Chen opened 3 years ago

Maggi-Chen commented 3 years ago

Hello Pierre,

I am running CONSENT-polish on a contig of ~10Mbp. I installed CONSENT v2.2.2 with conda. The commend was: CONSENT-polish --contigs $contig.fa --reads $read.fastq --out polished.fa

The alignment and sorting was successful. But I got an error at polishing step saying illegal instruction of CONSENT-polishing:

/data/user/maggic/anaconda2/envs/consent/bin/CONSENT-polish: line 197: 23038 Illegal instruction     CONSENT-polishing -a $tmpdir/"$alignments" -s "$minSupport" -S "$maxSupport" -l "$windowSize" -k "$merSize" -c "$commonKMers" -A "$minAnchors" -f "$solid" -m "$windowOverlap" -j "$nproc" -r "$contigs" -R "$reads" -M "$maxMSA" -p "$LRSCf" >> "$out"

Then I checked the CONSENT-polishing with CONSENT-polishing -h and I noticed there is no options like -r or -R, and the -m option seems not matching: 

CONSENT-polishing -h
Usage: CONSENT-polishing [-a alignmentFile.paf] [-k merSize] [-s minSupportForGoodRegions] [-l minLengthForGoodRegions] 
[-f freqThresholdForKMers] [-e maxError] [-p freqThresholdForKPersFreqs] [-c freqThresholdForKPersCons]
 [-m mode (0 for regions, 1 for cluster)] [-j threadsNb]

So I tried manually starting polishing step by CONSENT-polishing -a Alignments_22661.paf >> polished.fa, and I got segmentation fault error:

slurm_script: line 37: 25624 Segmentation fault      CONSENT-polishing -a Alignments_22661.paf >> polished.fa

The job failed after only 8 seconds and the memory usage was 1.64MB (I requested over 90GB) so I don't think it was a memory issue. Then I tried providing the contig (-r) and read (-R) files to CONSENT-polishing and I got the same illegal instruction error. I also tried converting reads.fastq to reads.fa and it didn't work.

One thing interesting is, I have several contigs (all are ~10Mbp in length) and corresponding reads.fastq files. I tried to polish them with same default settings and same amount of resources. Some successfully completed while others failed with the illegal instruction error. I could not find out what are different between these datasets.

I uploaded 3 failed and 1 successful contig+read files here (read_1.fasta is used for polishing contig_1.fa, etc). These are PacBio CLR reads.

Do you have any idea what might be the reason? Thank you so much! Maggi

aswathyseb commented 2 years ago

I have exactly the same problem. Did you have any success?

Running CONSENT-polish gives illegal instruction . As you said many of the parameters are not part of CONSENT-polishing.

If I run CONSENT-polishing by itself, it gives segmentation fault error.