POLCA Sorting and indexing alignment error

[slmiles]

Hi,

I am trying to run POLCA but I am getting the error ' Sorting and indexing alignment file failed' midway through.

My command is:

polca.sh -a genome.fasta -r "reads.fastq.gz reads2.fastq.gz" -m 1G

and the output is:

/home/ubuntu/miniconda3/envs/trycycler/bin/bwa /home/ubuntu/miniconda3/envs/trycycler/bin/freebayes /home/ubuntu/miniconda3/envs/trycycler/bin/samtools [Thu Jan 13 15:30:04 UTC 2022] Creating BWA index for /home/ubuntu/polypolish/polished.fasta [Thu Jan 13 15:30:09 UTC 2022] Aligning reads to /home/ubuntu/polypolish/polished.fasta [Thu Jan 13 15:32:38 UTC 2022] Sorting and indexing alignment file [Thu Jan 13 15:32:38 UTC 2022] Sorting and indexing alignment file failed

Any idea how to resolve this? Thank you

[liaochenlanruo]

me too

[ls-19]

Hello,

I am also facing the same issue. I am trying to run POLCA to polish my ONT minion assembly with Illumina reads but it is failing at the indexing step.

My command is:

polca.sh -a genome.fasta -r "reads1.fastq.gz reads2.fastq.gz" -t 16 -m 1G

The output:

[Mon 25 Jul 09:48:08 BST 2022] Creating BWA index for /contigs.fasta [Mon 25 Jul 09:50:01 BST 2022] Aligning reads to /.contigs.fasta [Mon 25 Jul 10:38:21 BST 2022] Sorting and indexing alignment file [Mon 25 Jul 10:38:22 BST 2022] Sorting and indexing alignment file failed

I've used this quite a few times in the past but only recently coming up against this error.

Any help would be appreciated.

Thanks

[termithorbor]

I had the error as well. Reinstalling Masurca with Conda worked for me. https://anaconda.org/bioconda/masurca

[andreott]

Hey, I guess it is just a problem with the samtools version. polca uses the following line to call samtools sort: $SAMTOOLS sort -m $MEM -@ $NUM_THREADS <(samtools view -uhS $BASM.unSorted.sam) $BASM.alignSorted 2>>samtools.err && \

So this is using the old style of giving samtools the output prefix (here $BASM.alignSorted) as second positional argument. According to the samtools documentation history, this is not supported by samtools since version 1.3. So installing a samtools version <= 1.2 should solve this. Probably it would be worth to adjust the polca.sh to use the recent samtools interface using the keyword (-o) argument style

[fanvanf]

Hey, I guess it is just a problem with the samtools version. polca uses the following line to call samtools sort: $SAMTOOLS sort -m $MEM -@ $NUM_THREADS <(samtools view -uhS $BASM.unSorted.sam) $BASM.alignSorted 2>>samtools.err && \

So this is using the old style of giving samtools the output prefix (here ) as second positional argument. According to the samtools documentation history, this is not supported by samtools since version 1.3. So installing a samtools version <= 1.2 should solve this. Probably it would be worth to adjust the polca.sh to use the recent samtools interface using the keyword () argument style$BASM.alignSorted``-o

Yes,it does.To avoid reinstalling Masurca or reinstalling samtools<=1.2,the line code $SAMTOOLS view -uhS $BASM.unSorted.sam |samtools sort -m $M EM -@ $NUM_THREADS -o $BASM.alignSorted.bam 2>>samtools.err & &\ were instead of the original code $SAMTOOLS sort -m $MEM -@ $NUM_THREADS <(samtools view -uhS $BASM.unSorted.sam) $BASM.alignSorted 2>>samtools.err && \.It works well.

[vidsvur]

I'm still running into this error, despite the patch fix.

[AceM1188]

Was continuing to experience this same issue in spite of the aforementioned patch. An uninstall and reinstall via conda did the job for me