Hi all,
I got errors like below:
No,1
=============
2012-07-26 16:37:43] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-26 16:37:43] Checking for Bowtie
Bowtie version: 0.12.8.0
[2012-07-26 16:37:44] Checking for Samtools
Samtools version: 0.1.13.0
[2012-07-26 16:37:44] Checking for Bowtie index files
[2012-07-26 16:37:44] Checking for reference FASTA file
Warning: Could not find FASTA file hg19_c.fa
[2012-07-26 16:37:44] Reconstituting reference FASTA file from Bowtie index
Executing: /home/xiaoyu/bin/bowtie-inspect hg19_c > VVinfect0h/tmp/hg19_c.fa
[2012-07-26 16:42:49] Generating SAM header for hg19_c
format: fastq
quality scale: phred33 (default)
[2012-07-26 16:43:42] Reading known junctions from GTF file
[2012-07-26 16:43:54] Preparing reads
left reads: min. length=50, max. length=50, 49053373 kept reads (712587 discarded)
[2012-07-26 17:00:17] Creating transcriptome data files..
[2012-07-26 17:01:36] Building Bowtie index from hg19UCSC.fa
[2012-07-26 17:53:34] Mapping left_kept_reads to transcriptome hg19UCSC with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 460T3#
are you sure this is a FASTQ-int file?
Command: /home/xiaoyu/bin/bowtie -q -C --col-keepends -v 1 -k 60 -m 60 -S -p 2 --sam-nohead --max /dev/null VVinfect0h/tmp/hg19UCSC -
No2
==============
[2012-07-26 16:43:15] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-26 16:43:15] Checking for Bowtie
Bowtie version: 0.12.8.0
[2012-07-26 16:43:15] Checking for Samtools
Samtools version: 0.1.13.0
[2012-07-26 16:43:15] Checking for Bowtie index files
[2012-07-26 16:43:15] Checking for reference FASTA file
Warning: Could not find FASTA file hg19_c.fa
[2012-07-26 16:43:15] Reconstituting reference FASTA file from Bowtie index
Executing: /home/xiaoyu/bin/bowtie-inspect hg19_c > VVinfect4h/tmp/hg19_c.fa
[2012-07-26 16:48:16] Generating SAM header for hg19_c
format: fastq
quality scale: phred33 (default)
[2012-07-26 16:48:22] Reading known junctions from GTF file
[2012-07-26 16:48:33] Preparing reads
left reads: min. length=50, max. length=50, 34854552 kept reads (1262790 discarded)
[2012-07-26 16:59:38] Creating transcriptome data files..
[2012-07-26 17:01:05] Building Bowtie index from hg19UCSC.fa
[2012-07-26 17:51:34] Mapping left_kept_reads to transcriptome hg19UCSC with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 51300T13
are you sure this is a FASTQ-int file?
Command: /home/xiaoyu/bin/bowtie -q -C --col-keepends -v 1 -k 60 -m 60 -S -p 2 --sam-nohead --max /dev/null VVinfect4h/tmp/hg19UCSC -
How to fix it? Is it possible to trimm the reads "460T3#" "51300T13" out? If yes, how? Please help.
I got errors like below:
No,1
=============
2012-07-26 16:37:43] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-26 16:37:43] Checking for Bowtie
Bowtie version: 0.12.8.0
[2012-07-26 16:37:44] Checking for Samtools
Samtools version: 0.1.13.0
[2012-07-26 16:37:44] Checking for Bowtie index files
[2012-07-26 16:37:44] Checking for reference FASTA file
Warning: Could not find FASTA file hg19_c.fa
[2012-07-26 16:37:44] Reconstituting reference FASTA file from Bowtie index
Executing: /home/xiaoyu/bin/bowtie-inspect hg19_c > VVinfect0h/tmp/hg19_c.fa
[2012-07-26 16:42:49] Generating SAM header for hg19_c
format: fastq
quality scale: phred33 (default)
[2012-07-26 16:43:42] Reading known junctions from GTF file
[2012-07-26 16:43:54] Preparing reads
left reads: min. length=50, max. length=50, 49053373 kept reads (712587 discarded)
[2012-07-26 17:00:17] Creating transcriptome data files..
[2012-07-26 17:01:36] Building Bowtie index from hg19UCSC.fa
[2012-07-26 17:53:34] Mapping left_kept_reads to transcriptome hg19UCSC with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 460T3#
are you sure this is a FASTQ-int file?
Command: /home/xiaoyu/bin/bowtie -q -C --col-keepends -v 1 -k 60 -m 60 -S -p 2 --sam-nohead --max /dev/null VVinfect0h/tmp/hg19UCSC -
No2
==============
[2012-07-26 16:43:15] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-26 16:43:15] Checking for Bowtie
Bowtie version: 0.12.8.0
[2012-07-26 16:43:15] Checking for Samtools
Samtools version: 0.1.13.0
[2012-07-26 16:43:15] Checking for Bowtie index files
[2012-07-26 16:43:15] Checking for reference FASTA file
Warning: Could not find FASTA file hg19_c.fa
[2012-07-26 16:43:15] Reconstituting reference FASTA file from Bowtie index
Executing: /home/xiaoyu/bin/bowtie-inspect hg19_c > VVinfect4h/tmp/hg19_c.fa
[2012-07-26 16:48:16] Generating SAM header for hg19_c
format: fastq
quality scale: phred33 (default)
[2012-07-26 16:48:22] Reading known junctions from GTF file
[2012-07-26 16:48:33] Preparing reads
left reads: min. length=50, max. length=50, 34854552 kept reads (1262790 discarded)
[2012-07-26 16:59:38] Creating transcriptome data files..
[2012-07-26 17:01:05] Building Bowtie index from hg19UCSC.fa
[2012-07-26 17:51:34] Mapping left_kept_reads to transcriptome hg19UCSC with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 51300T13
are you sure this is a FASTQ-int file?
Command: /home/xiaoyu/bin/bowtie -q -C --col-keepends -v 1 -k 60 -m 60 -S -p 2 --sam-nohead --max /dev/null VVinfect4h/tmp/hg19UCSC -
How to fix it? Is it possible to trimm the reads "460T3#" "51300T13" out? If yes, how? Please help.
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