Originally posted in the old forum by Cecilia on 23.05.2012 - 21:52
I tried to run 'filterBam --uniq --paired --in input.bam --out filtered.bam'. The process has been running for more than 1 day and still not finished. The output file is empty.
How long usually does filterBam take to run?
The input.bam file was generated by Tophat. 'samtools flagstat input.bam' showed
1675091 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
1675091 + 0 mapped (100.00%:-nan%)
1675091 + 0 paired in sequencing
828443 + 0 read1
846648 + 0 read2
1478028 + 0 properly paired (88.24%:-nan%)
....
filterBam execution time
Moderator: bioinf
Re: filterBam execution time
by katharina on 23.05.2012 - 22:57
Did you name the read pairs with a dash (-1, -2) instead of a slash (/1, /2) to indicate pairdness? Tophat/Bowtie cleave off the slash numbers, which means that filterBam will try for a veeeery long time to identify impossible pairs. This should eventually result in a segmentation fault.
Use "samtools view" to inspect the tophat output and make sure that the -1, -2 is present.
I'll post some example runtimes of filterBam on different file sizes next week.
Did you name the read pairs with a dash (-1, -2) instead of a slash (/1, /2) to indicate pairdness? Tophat/Bowtie cleave off the slash numbers, which means that filterBam will try for a veeeery long time to identify impossible pairs. This should eventually result in a segmentation fault.
Use "samtools view" to inspect the tophat output and make sure that the -1, -2 is present.
I'll post some example runtimes of filterBam on different file sizes next week.
Re: filterBam execution time
by Cecilia on 24.05.2012 - 02:29
You're right. Tophat chopped off the /1 and /2 part so the read ID became something like 'HWIST945:92:d059facxx:5:1205:7877:128128'. How does 'samtools flagstat' tell whether the alignment is for read1 or read2? Since the stats show no duplicate, can I just obmit the filterBam step?
You're right. Tophat chopped off the /1 and /2 part so the read ID became something like 'HWIST945:92:d059facxx:5:1205:7877:128128'. How does 'samtools flagstat' tell whether the alignment is for read1 or read2? Since the stats show no duplicate, can I just obmit the filterBam step?
Re: filterBam execution time
by katharina on 29.05.2012 - 10:14
Tophat (or rather Bowtie) can directly produced "paired alignments". Our filterBam and bam2hints tools currently do not work with the paired bam format. Therefore, you'll need to run Tophat/Bowtie in 'single mode' and use the -1/-2 read pair name convention.
You can omit filterBam but this will produce hints of lower quality. (And you cannot use native paired bam output format from Tophat/Bowtie, as mentioned above.)
Tophat (or rather Bowtie) can directly produced "paired alignments". Our filterBam and bam2hints tools currently do not work with the paired bam format. Therefore, you'll need to run Tophat/Bowtie in 'single mode' and use the -1/-2 read pair name convention.
You can omit filterBam but this will produce hints of lower quality. (And you cannot use native paired bam output format from Tophat/Bowtie, as mentioned above.)
Re: filterBam execution time
by katharina on 29.05.2012 - 10:24
The execution time for filterBam with --uniq and --paired flag took about 40 minutes for a 8.8 GB bam file on a Intel(R) Xeon(R) CPU 3.07GHz.
The execution time for filterBam with --uniq and --paired flag took about 40 minutes for a 8.8 GB bam file on a Intel(R) Xeon(R) CPU 3.07GHz.
Re: filterBam execution time
by -C on 15.12.2012 - 01:11
filterBam background jobs processing
When running filterBam the output is displayed in the terminal and once you run the job in the background you cannot disown it. Is there a command I can add to fix this?
filterBam background jobs processing
When running filterBam the output is displayed in the terminal and once you run the job in the background you cannot disown it. Is there a command I can add to fix this?
Re: filterBam execution time
by katharina on 18.12.2012 - 12:31
Can you please post your exact program call?
Katharina
Can you please post your exact program call?
Katharina
Re: filterBam execution time
by -C on 21.12.2012 - 22:50
filterBam background jobs processing
I figured it out. thanks for the response.
filterBam background jobs processing
I figured it out. thanks for the response.