I've been generating BAM files using the STAR command below:
for ((i=102; i<=305; i++)); do ./STAR --readFilesIn fastq/E08/SRR2930$i.fastq --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outSAMmultNmax 1 --genomeDir STARindex --twopassMode Basic --runThreadN 12 --outFileNamePrefix 2930$i; done
My fastq files are about 180mb and generated BAM files are about 75kb. I checked BAM files using
samtools stats --split RG 2930107Aligned.sortedByCoord.out.bam | grep '^SN' and saw the following output for all BAM files:
SN raw total sequences: 0 SN filtered sequences: 0 SN sequences: 0 SN is sorted: 1 SN 1st fragments: 0 SN last fragments: 0 SN reads mapped: 0 SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped SN reads unmapped: 0 SN reads properly paired: 0 # proper-pair bit set SN reads paired: 0 # paired-end technology bit set SN reads duplicated: 0 # PCR or optical duplicate bit set SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 SN total length: 0 # ignores clipping SN bases mapped: 0 # ignores clipping SN bases mapped (cigar): 0 # more accurate SN bases trimmed: 0 SN bases duplicated: 0 SN mismatches: 0 # from NM fields SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) SN average length: 0 SN maximum length: 30 SN average quality: 0.0 SN insert size average: 0.0 SN insert size standard deviation: 0.0 SN inward oriented pairs: 0 SN outward oriented pairs: 0 SN pairs with other orientation: 0 SN pairs on different chromosomes: 0
Also, when I run
samtools view 2930107Aligned.sortedByCoord.out.bam command, nothing shows up in terminal.
So, I was wondering what might be cause for the problem here, fastq files themselves or the code that generates BAM files? I know that the question is quite vague, sorry for that, but I'm not sure where to look at to solve the problem.
Edit: Thanks a lot for your helps. I've run a single file, STAR worked without any problems on terminal.
./STAR --readFilesIn fastq/E08/SRR2930160.fastq --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outSAMmultNmax 1 --genomeDir STARindex --twopassMode Basic --runThreadN 12 --outFileNamePrefix 2930160 Apr 04 15:55:10 ..... started STAR run Apr 04 15:55:10 ..... loading genome Apr 04 15:55:26 ..... started 1st pass mapping Apr 04 15:55:29 ..... finished 1st pass mapping Apr 04 15:55:30 ..... inserting junctions into the genome indices Apr 04 15:57:23 ..... started mapping Apr 04 15:57:26 ..... finished mapping Apr 04 15:57:27 ..... started sorting BAM Apr 04 15:57:27 ..... finished successfully
And here is the log.
Edit 2: I asked about this issue to STAR developers on github and apparently my data is from Solid sequencer and STAR does not support that, here is a link to the issue. Thanks a lot for all comments though, cheers.