apeltzer
commented
2 years ago Please use nf-core/eager to analyze your data and then come back there if there is an issue with using dedup 👍🏻 This should reduce the amount of potential error substantially :-)
I’m running a sample with EAGER and I want to get no-merged data, following the instructions below: -For the input file upload two Fasq (reads 1 e 2) and select the Single-End Data -General settings:
FastQC analysis;
Adapter RM/Merging : CLIP&Merge (Perform only adapter clipping);
Mapping: CircularMapper;
Complexity Estimation;
Remove Duplicates with DeDup;
Damage calculation with mapDamage;
But the analysis dies when trying to remove the duplicates. The .log file reports:
SamtoolsSortDeDup was executed with the following commandline: “samtools sort -[@ 10]() -m 3G /../OUTPUT/5-DeDup/file_name.fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.bam -o /../ OUTPUT/INPUT/5-DeDup/file_name.fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.sorted.bam “
“samtools sort: truncated file. Aborting”
Furthermore I can still find the following 10 multiple bam files in the 5-DeDup directory even if they should disappear once the final file(file_name.fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.sorted.bam. ) is created:
-fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.sorted.bam.tmp.0000.bam ( this is an example of one of the 10 files)
How can I manage this issue?
Should I start again the analysis from the beginning or is there a way to skip the steps that went right?
I was also wandering if there is a way to know if the 10 files in the 5-DeDup directory are complete.
Lastly, I only manage to get the report file if I run more samples in a row, how can I get it analysing only one file?