Hi,
I am a student trying my hand at bioinformatics. While performing an analysis I got the following output:
[2014-11-04 11:54:56] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2014-11-04 11:54:56] Checking for Bowtie
Bowtie version: 2.1.0.0
[2014-11-04 11:54:56] Checking for Samtools
Samtools version: 0.1.19.0
[2014-11-04 11:54:56] Checking for Bowtie index files (genome)..
Found both Bowtie1 and Bowtie2 indexes.
[2014-11-04 11:54:56] Checking for reference FASTA file
[2014-11-04 11:54:56] Generating SAM header for genome
format: fastq
quality scale: phred33 (default)
[2014-11-04 11:54:57] Reading known junctions from GTF file
[2014-11-04 11:55:01] Preparing reads
left reads: min. length=76, max. length=101, 946251048 kept reads (4766237 discarded)
right reads: min. length=76, max. length=101, 945724834 kept reads (5292451 discarded)
[2014-11-04 19:36:04] Building transcriptome data files..
[2014-11-04 19:36:37] Building Bowtie index from genes.fa
[2014-11-04 19:46:42] Mapping left_kept_reads to transcriptome genes with Bowtie2
[2014-11-06 20:19:53] Mapping right_kept_reads to transcriptome genes with Bowtie2
[2014-11-08 21:00:22] Resuming TopHat pipeline with unmapped reads
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
[2014-11-08 21:00:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
[2014-11-10 09:23:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2014-11-10 16:29:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2014-11-10 22:21:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2014-11-11 13:25:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
and so on. The test file went of without a hitch. I am thinking it may have something to do with the size of the reads(100 files, 545.1GB) Can anyone help me with this?
I am a student trying my hand at bioinformatics. While performing an analysis I got the following output:
[2014-11-04 11:54:56] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2014-11-04 11:54:56] Checking for Bowtie
Bowtie version: 2.1.0.0
[2014-11-04 11:54:56] Checking for Samtools
Samtools version: 0.1.19.0
[2014-11-04 11:54:56] Checking for Bowtie index files (genome)..
Found both Bowtie1 and Bowtie2 indexes.
[2014-11-04 11:54:56] Checking for reference FASTA file
[2014-11-04 11:54:56] Generating SAM header for genome
format: fastq
quality scale: phred33 (default)
[2014-11-04 11:54:57] Reading known junctions from GTF file
[2014-11-04 11:55:01] Preparing reads
left reads: min. length=76, max. length=101, 946251048 kept reads (4766237 discarded)
right reads: min. length=76, max. length=101, 945724834 kept reads (5292451 discarded)
[2014-11-04 19:36:04] Building transcriptome data files..
[2014-11-04 19:36:37] Building Bowtie index from genes.fa
[2014-11-04 19:46:42] Mapping left_kept_reads to transcriptome genes with Bowtie2
[2014-11-06 20:19:53] Mapping right_kept_reads to transcriptome genes with Bowtie2
[2014-11-08 21:00:22] Resuming TopHat pipeline with unmapped reads
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
[2014-11-08 21:00:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
[2014-11-10 09:23:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2014-11-10 16:29:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2014-11-10 22:21:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2014-11-11 13:25:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
and so on. The test file went of without a hitch. I am thinking it may have something to do with the size of the reads(100 files, 545.1GB) Can anyone help me with this?
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