TopHat v1.1.4 - Error: could not convert to BAM with samtools

[ben.weisburd]

I'm running TopHat with the following options:

tophat --keep-tmp --solexa1.3-quals --butterfly-search --min-intron-length 10 --max-intron-length 20000

and getting an error at the very end. This only happens on 1 out 4 of my data files.

[Fri Nov 26 02:19:27 2010] Beginning TopHat run (v1.1.4)
-----------------------------------------------
[Fri Nov 26 02:19:27 2010] Preparing output location ./tophat_out/
[Fri Nov 26 02:19:27 2010] Checking for Bowtie index files
[Fri Nov 26 02:19:27 2010] Checking for reference FASTA file
[Fri Nov 26 02:19:27 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Nov 26 02:19:27 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Fri Nov 26 02:19:27 2010] Checking reads
min read length: 20bp, max read length: 80bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)

[Fri Nov 26 02:24:48 2010] Mapping reads against merlin with Bowtie
[Fri Nov 26 02:35:18 2010] Joining segment hits
[Fri Nov 26 02:40:36 2010] Mapping reads against merlin with Bowtie(1/3)
[Fri Nov 26 02:46:23 2010] Mapping reads against merlin with Bowtie(2/3)
[Fri Nov 26 02:53:25 2010] Mapping reads against merlin with Bowtie(3/3)
[Fri Nov 26 02:53:29 2010] Searching for junctions via segment mapping
[Fri Nov 26 03:01:00 2010] Retrieving sequences for splices
[Fri Nov 26 03:01:01 2010] Indexing splices
[Fri Nov 26 03:01:06 2010] Mapping reads against segment_juncs with Bowtie
[Fri Nov 26 03:10:01 2010] Mapping reads against segment_juncs with Bowtie
[Fri Nov 26 03:20:37 2010] Mapping reads against segment_juncs with Bowtie
[Fri Nov 26 03:20:47 2010] Joining segment hits
[Fri Nov 26 03:22:15 2010] Reporting output tracks
Error: could not convert to BAM with samtools

I can work around it by doing the steps below, so just posting in case others run into this.

# Fix the SO:sorted header
sed s/sorted/unsorted/ tophat_out/tmp/accepted_hits.sam > fixed.sam

# Use picard to fix clipping
java -jar picard-tools-1.35/CleanSam.jar INPUT=fixed.sam OUTPUT=fixed2.sam

# Convert to bam
java -jar picard-tools-1.35/SortSam.jar INPUT=fixed2.sam OUTPUT=accepted_hits.bam SORT_ORDER=coordinate

[Daehwan]

This is a bug in TopHat, we fixed this and will post a new version soon.

Thanks,
Daehwan

[ali.stanford]

I am getting a similar error, but I am running Tophat v1.2.0. The Tophat release note say a compatibility issue was fixed with samtools version 0.1.12a, which is what I am using. Any ideas?

This is the error report:

Error in tophat:

[Tue Mar 8 14:09:27 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Tue Mar 8 14:09:27 2011] Preparing output location /home/lib/galaxy/database/tmp/tmplfhKIQ/

[Tue Mar 8 14:09:27 2011] Checking for Bowtie index files
[Tue Mar 8 14:09:27 2011] Checking for reference FASTA file

Warning: Could not find FASTA file /home/lib/galaxy/hg18/bowtie/base/hg18.fa
[Tue Mar 8 14:09:27 2011] Reconstituting reference FASTA file from Bowtie index

[Tue Mar 8 14:13:47 2011] Checking for Bowtie

Bowtie version: 0.12.7.0
[Tue Mar 8 14:13:47 2011] Checking for Samtools

Samtools Version: 0.1.12a
[Tue Mar 8 14:14:31 2011] Checking reads

min read length: 75bp, max read length: 75bp
format: fastq
quality scale: phred33 (default)
[Tue Mar 8 14:32:10 2011] Mapping reads against hg18 with Bowtie
[Tue Mar 8 14:48:27 2011] Joining segment hits
[Tue Mar 8 14:55:57 2011] Mapping reads against hg18 with Bowtie(1/3)

[Tue Mar 8 15:09:23 2011] Mapping reads against hg18 with Bowtie(2/3)
[Tue Mar 8 15:22:17 2011] Mapping reads against hg18 with Bowtie(3/3)
[Tue Mar 8 15:34:25 2011] Mapping reads against hg18 with Bowtie
[Tue Mar 8 15:50:05 2011] Joining segment hits

[Tue Mar 8 15:57:38 2011] Mapping reads against hg18 with Bowtie(1/3)
[Tue Mar 8 16:12:02 2011] Mapping reads against hg18 with Bowtie(2/3)
[Tue Mar 8 16:25:40 2011] Mapping reads against hg18 with Bowtie(3/3)

[Tue Mar 8 16:38:24 2011] Searching for junctions via segment mapping
[Tue Mar 8 17:07:34 2011] Retrieving sequences for splices
[Tue Mar 8 17:12:50 2011] Indexing splices
[Tue Mar 8 17:25:47 2011] Mapping reads against segment_juncs with Bowtie

[Tue Mar 8 17:36:01 2011] Mapping reads against segment_juncs with Bowtie
[Tue Mar 8 17:46:22 2011] Mapping reads against segment_juncs with Bowtie
[Tue Mar 8 17:56:13 2011] Joining segment hits
[Tue Mar 8 18:14:16 2011] Mapping reads against segment_juncs with Bowtie

[Tue Mar 8 18:25:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue Mar 8 18:35:59 2011] Mapping reads against segment_juncs with Bowtie
[Tue Mar 8 18:46:09 2011] Joining segment hits
[Tue Mar 8 19:02:35 2011] Reporting output tracks

Error: could not convert to BAM with samtools

[jgoecks]

Yes, I am seeing this problem in Tophat v1.2.0 as well, using samtools 0.1.12a. I have not been able to fix it as of yet; any help would be greatly appreciated.

[waseem]

This is a bug in TopHat, we fixed this and will post a new version soon.

Thanks,
Daehwan

Has it been done, I am getting the same error