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Old 11-28-2011, 08:03 AM   #1
feng
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Default broken pipe during tophat analysis

Hi Does anyone know what problem with my analysis?

../../Program/tophat/tophat -p 12 ../../Database/bowtie-index/human_g1k_v37 ../../Data/MCC/MCC3154.fastq

[Mon Nov 28 11:39:27 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Mon Nov 28 11:39:27 2011] Preparing output location ./tophat_out/
[Mon Nov 28 11:39:27 2011] Checking for Bowtie index files
[Mon Nov 28 11:39:27 2011] Checking for reference FASTA file
[Mon Nov 28 11:39:27 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Nov 28 11:39:27 2011] Checking for Samtools
Samtools Version: 0.1.18
[Mon Nov 28 11:39:27 2011] Generating SAM header for ../../Database/bowtie-index/human_g1k_v37
[Mon Nov 28 11:39:29 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
Left reads: min. length=31, count=216599
[Mon Nov 28 11:39:48 2011] Mapping left_kept_reads against human_g1k_v37 with Bowtie
[Mon Nov 28 11:40:12 2011] Processing bowtie hits
[Mon Nov 28 11:42:18 2011] Mapping left_kept_reads_seg1 against human_g1k_v37 with Bowtie (1/17)
....
[Mon Nov 28 11:44:45 2011] Mapping left_kept_reads_seg17 against human_g1k_v37 with Bowtie (17/17)
[Mon Nov 28 11:44:47 2011] Searching for junctions via segment mapping
[Mon Nov 28 11:47:04 2011] Retrieving sequences for splices
[Mon Nov 28 11:51:45 2011] Indexing splices
[Mon Nov 28 11:51:49 2011] Mapping left_kept_reads_seg1 against segment_juncs with Bowtie (1/17)
....
[Mon Nov 28 11:53:01 2011] Mapping left_kept_reads_seg17 against segment_juncs with Bowtie (17/17)
[Mon Nov 28 11:53:05 2011] Joining segment hits
sort: write failed: standard output: Broken pipe
sort: write error
[Mon Nov 28 11:55:11 2011] Reporting output tracks
-----------------------------------------------
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Old 11-28-2011, 10:33 AM   #2
cjp
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Default

Copied and pasted from my previous answer to debug failed TopHat runs: http://seqanswers.com/forums/showthread.php?t=14140

When debugging failed TopHat runs, you can also try to run the individual commands from the command line yourself.

In the logs/ sub-directory of your output directory there should be a file called run.log which shows the commands that TopHat runs. There are also other log files in there - look to see if you can find errors (especially in the newest one or two files). Otherwise try running each command by itself from the directory you started TopHat in and see if and where empty files are made. The tmp stuff needed to do this is usually kept if a run fails.

Chris
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Old 11-28-2011, 11:33 AM   #3
feng
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Posts: 50
Default it drops here

/Volumes/Voyager/Package/Program/tophat/samtools view ./tophat_out/tmp/left_kept_reads.unspl.bam | sort -k1,1n -m -T./tophat_out/tmp/ - ./tophat_out/tmp/left_kept_reads_3192.sam.merge_sort.fifo | /Volumes/Voyager/Package/Program/tophat/samtools view -S -b - > ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam


after

/Volumes/Voyager/Package/Program/tophat/samtools view -S -b - > ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam


What is wrong with samtools view?

[samopen] SAM header is present: 84 sequences.
[sam_read1] reference '6012' is recognized as '*'.
Parse warning at line 223: mapped sequence without CIGAR
Parse error at line 223: sequence and quality are inconsistent
Abort trap
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