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I have hit an error trying to run one of the test datasets that merges multiple fastq files per sample (samplesheet.multi_lanes.csv).
I have to say first that when running with the testing dataset that includes only the chr17.fa the pipeline runs great. When i run it with my local version of the hg38 igenomes fasta however it hits an error at the GroupReadsByUmi step. The file should be accessible by downloading the hg38 version in this link - here.
I download the sample sheet from the test-dataset repo and I run the pipeline using:
nextflow run nf-core/fastquorum -r 1.0.0 -params-file params.yaml -w work.nobackup -resume
When I track down the merged bam one level more I reach the MERGE_BAM process. The individual bams seem to be all sorted correctly but the merged one (see above) may not be?
Description of the bug
Hi
I have hit an error trying to run one of the test datasets that merges multiple fastq files per sample (
samplesheet.multi_lanes.csv
).I have to say first that when running with the testing dataset that includes only the
chr17.fa
the pipeline runs great. When i run it with my local version of thehg38
igenomes fasta however it hits an error at the GroupReadsByUmi step. The file should be accessible by downloading the hg38 version in this link - here.I download the sample sheet from the test-dataset repo and I run the pipeline using:
And the
params.yaml
file is:The error is in the
GroupReadsByUmi
step, it claims that a given read is not sorted correctly (SRR6109255.382418
).When going into the directory I can see that the problematic read (the first read in the file) is actually properly paired but and not in order?
When I track down the merged bam one level more I reach the
MERGE_BAM
process. The individual bams seem to be all sorted correctly but the merged one (see above) may not be?I am not sure if I am doing smth wrong.
Command used and terminal output
Relevant files
No response
System information
HPC, running on SGE
Ubuntu Linux
N E X T F L O W
version 24.04.1 build 5913
created 20-05-2024 09:48 UTC (02:48 PDT)
cite doi:10.1038/nbt.3820
http://nextflow.io
nf-core/fastquorum = 1.0.0
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