Dear colleagues,
I'm using tophat 2.0.6 to RNASeq data. I'm usign all the default options and setting -p 12.
I consistently get the error below.
Several threads in this forums suggest that setting the number of threads to 1 (-p 1) takes care of this problem for tophat versions up to 2.0.4.
Does anyone know if the problem persists in version tophat 2.0.6 and if so is there a workaround other than setting threads to 1? this will dramatically increase the runtime and make usage of resources wasteful.
Thank you all.
Kike
[2013-04-12 23:01:08] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-04-12 23:01:08] Checking for Bowtie
Bowtie version: 2.0.2.0
[2013-04-12 23:01:08] Checking for Samtools
Samtools version: 0.1.18.0
[2013-04-12 23:01:08] Checking for Bowtie index files
[2013-04-12 23:01:08] Checking for reference FASTA file
Warning: Could not find FASTA file /data/zudairee/bowtie2_indexes/mm10/mm10.fa
[2013-04-12 23:01:08] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/apps/bowtie/2-2.0.2/bowtie2-inspect /data/zudairee/bowtie2_indexes/mm10/mm10 > /data/zudairee/unaligned/TophatTwoResult-041213-6/tmp/mm10.fa
[2013-04-12 23:04:21] Generating SAM header for /data/zudairee/bowtie2_indexes/mm10/mm10
format: fastq
quality scale: phred33 (default)
[2013-04-12 23:08:28] Preparing reads
left reads: min. length=101, max. length=101, 3999983 kept reads (17 discarded)
right reads: min. length=101, max. length=101, 3999744 kept reads (256 discarded)
[2013-04-12 23:14:39] Mapping left_kept_reads to genome mm10 with Bowtie2
[2013-04-12 23:24:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2013-04-12 23:29:56] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2013-04-12 23:35:39] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2013-04-12 23:41:03] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2013-04-12 23:47:01] Mapping right_kept_reads to genome mm10 with Bowtie2
[2013-04-12 23:57:30] Mapping right_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2013-04-13 00:02:59] Mapping right_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2013-04-13 00:09:00] Mapping right_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2013-04-13 00:14:19] Mapping right_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2013-04-13 00:19:41] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =1
Error: could not get read# 3671535 from stream!Error: could not get read# 322609 from stream!!Error: could not get read# 1657762 from stream!
I'm using tophat 2.0.6 to RNASeq data. I'm usign all the default options and setting -p 12.
I consistently get the error below.
Several threads in this forums suggest that setting the number of threads to 1 (-p 1) takes care of this problem for tophat versions up to 2.0.4.
Does anyone know if the problem persists in version tophat 2.0.6 and if so is there a workaround other than setting threads to 1? this will dramatically increase the runtime and make usage of resources wasteful.
Thank you all.
Kike
[2013-04-12 23:01:08] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-04-12 23:01:08] Checking for Bowtie
Bowtie version: 2.0.2.0
[2013-04-12 23:01:08] Checking for Samtools
Samtools version: 0.1.18.0
[2013-04-12 23:01:08] Checking for Bowtie index files
[2013-04-12 23:01:08] Checking for reference FASTA file
Warning: Could not find FASTA file /data/zudairee/bowtie2_indexes/mm10/mm10.fa
[2013-04-12 23:01:08] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/apps/bowtie/2-2.0.2/bowtie2-inspect /data/zudairee/bowtie2_indexes/mm10/mm10 > /data/zudairee/unaligned/TophatTwoResult-041213-6/tmp/mm10.fa
[2013-04-12 23:04:21] Generating SAM header for /data/zudairee/bowtie2_indexes/mm10/mm10
format: fastq
quality scale: phred33 (default)
[2013-04-12 23:08:28] Preparing reads
left reads: min. length=101, max. length=101, 3999983 kept reads (17 discarded)
right reads: min. length=101, max. length=101, 3999744 kept reads (256 discarded)
[2013-04-12 23:14:39] Mapping left_kept_reads to genome mm10 with Bowtie2
[2013-04-12 23:24:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2013-04-12 23:29:56] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2013-04-12 23:35:39] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2013-04-12 23:41:03] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2013-04-12 23:47:01] Mapping right_kept_reads to genome mm10 with Bowtie2
[2013-04-12 23:57:30] Mapping right_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2013-04-13 00:02:59] Mapping right_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2013-04-13 00:09:00] Mapping right_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2013-04-13 00:14:19] Mapping right_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2013-04-13 00:19:41] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =1
Error: could not get read# 3671535 from stream!Error: could not get read# 322609 from stream!!Error: could not get read# 1657762 from stream!
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