leepc12
commented
6 years ago Pipeline keeps dupmark log (.dup.qc) but .dupmark.bam is an intermediate file and it's deleted at the end of the filtering step. It's just okay that you cannot find it.
I think there is another reason for this error like lack of space on your output directory or /tmp? Can you check if you have enough space on output directory (./out) and $TMP and $TMPDIR(/tmp)?
Also, can you post a full error log here?
On Sun, Oct 29, 2017 at 1:59 PM, Alberto Riva notifications@github.com wrote:
I'm running the atacqc pipeline on 3 paired-end fastq files, and I'm getting an error because samtools cannot find the dupmark.bam file. I'm looking in the log file to see what the problem could be, and this is the command that (if I'm not mistaken) should create this file:
| 14746 | running (RUNNING) | dedup_bam_PE_1 rep3 | | if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u /DATA/runs/miami/atacqcsplit. out/align/rep3/3-UMC25-Ctrl_R1.PE2SE.bam |; sambamba sort -t 5 -n /dev/stdin -o /DATA/runs/miami/atacqcsplit.out/align/rep3/3-UMC25-Ctrl_R1.PE2SE.dupmark.bam;; samtools view -h /DATA/runs/miami/atacqcsplit.out/align/rep3 |
I also see messages produced by picard MarkDuplicates in the log file, and it seems to run successfully, but indeed the dupmark.bam file is not there. How and where can I find more information to understand where the problem is?
Thank you!
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albertoriva
I'm running the atacqc pipeline on 3 paired-end fastq files, and I'm getting an error because samtools cannot find the dupmark.bam file. I'm looking in the log file to see what the problem could be, and this is the command that (if I'm not mistaken) should create this file:
| 14746 | running (RUNNING) | dedup_bam_PE_1 rep3 | | if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u /DATA/runs/miami/atacqcsplit.out/align/rep3/3-UMC25-Ctrl_R1.PE2SE.bam |; sambamba sort -t 5 -n /dev/stdin -o /DATA/runs/miami/atacqcsplit.out/align/rep3/3-UMC25-Ctrl_R1.PE2SE.dupmark.bam;; samtools view -h /DATA/runs/miami/atacqcsplit.out/align/rep3 |
I also see messages produced by picard MarkDuplicates in the log file, and it seems to run successfully, but indeed the dupmark.bam file is not there. How and where can I find more information to understand where the problem is?
Thank you!