Tophat : [Main_Samview] Truncated File

Question

[Nicolas Rosewick]

Hi,

After running tophat 2.04 with fusion-search (bowtie 1), I wanted to convert the accepted_hits.sam (I put --no-convert-bam param on) to a bam file. So I did :

samtools -bS accepted_hits.sam > accepted_hits.bam
[main_samview]truncated file

here's my tophat command :

tophat -r 60 --b2-sensitive --no-convert-bam --splice-mismatches 1 --min-anchor-length 5 --fusion-search --segment-length 20 --bowtie1 --no-coverage-search --fusion-anchor-length 13 --fusion-min-dist 100000 --mate-std-dev 70 --library-type fr-unstranded --output-dir tophat_2_fusion /home/lab/database/bowtie/ref R1.fastq.gz R2.fastq.gz

After checking in the log file reports.samtools_sort.log0

[bam_sort_core] merging from 23 files...

But I have 28 chromosomes ... indeed when checking the report.log :

tophat_reports v2.0.4 (3480M)
---------------------------------------
[samopen] SAM header is present: 28 sequences.    
    Loading chr10...done
    Loading chr11...done
    Loading chr12...done
    Loading chr13...done
    Loading chr14...done
    Loading chr15...done
    Loading chr16...done
    Loading chr17...done
    Loading chr18...done
    Loading chr19...done
    Loading chr1...done
    Loading chr20...done
    Loading chr21...done
    Loading chr22...done
    Loading chr23...done
    Loading chr24...done
    Loading chr25...done
    Loading chr26...done
    Loading chr27...done
    Loading chr2...done
    Loading chr3...done
    Loading chr4...done
    Loading chr5...done
    Loading chr6...done
    Loading chr7...done
    Loading chr8...done
    Loading chr9...done
    Loading chrX...done
    Loading ...done
Loaded 118271 junctions
Reporting final accepted alignments...done.
Printing junction BED track...done
Printing insertions...done
Printing deletions...done
Printing fusions...done
Found 73588 junctions from happy spliced reads

So in my sam file there is no alignment on 5 chr ... and that's a problem (...)

Other thing in the tophat.log, here are the last lines of the file :

[2012-08-30 09:22:07] Reporting output tracks
Warning: couldn't remove all temporary files in tophat_2_fusion/tmp/
-----------------------------------------------
[2012-08-30 11:13:15] Run complete: 1 days 01:56:41 elapsed

Anyone can help me ?

thanks,

N.

[JC]

duplicated: http://biostars.org/post/show/52074/tophat2-error-segment-based-junction-search-failed-with-err-11/

[Nicolas Rosewick]

no it's not the same. here tophat finished well.

Answer 1

[JC]

I think the BAM merging is reported by files, not chromosomes (some chromosomes can be mixed in one file to save space).

Did you check if you have enough disk space during the running? Tophat produces a lot of big files, I have similar problems before because during the running my hard disk fills the quota and the files became truncated.

[Nicolas Rosewick]

I contact the guy who is in charge of the grid server and indeed the problem is coming from there (file size limit)