any idea about this failure? how to make fasta have the same length? and what does this mean? thank you!
[Wed Sep 28 20:19:22 2011] Beginning transcriptome assembly merge
-------------------------------------------
[Wed Sep 28 20:19:22 2011] Preparing output location ./merged_asm/
[Wed Sep 28 20:19:22 2011] Converting GTF files to SAM
gtf_to_sam: /usr/lib64/libz.so.1: no version information available (required by gtf_to_sam)
[20:19:22] Loading reference annotation.
gtf_to_sam: /usr/lib64/libz.so.1: no version information available (required by gtf_to_sam)
[20:19:22] Loading reference annotation.
gtf_to_sam: /usr/lib64/libz.so.1: no version information available (required by gtf_to_sam)
[20:19:23] Loading reference annotation.
[Wed Sep 28 20:19:23 2011] Quantitating transcripts
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
You are using Cufflinks v1.1.0, which is the most recent release.
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_fileu98BBT doesn't appear to be a valid BAM file, trying SAM...
[20:19:23] Loading reference annotation.
[20:19:24] Inspecting reads and determining fragment length distribution.
Processed 4610 loci.
> Map Properties:
> Total Map Mass: 27713.00
> Read Type: 0bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[20:19:24] Assembling transcripts and estimating abundances.
Processed 4610 loci.
[Wed Sep 28 20:19:53 2011] Comparing against reference file xxx.gtf
You are using Cufflinks v1.1.0, which is the most recent release.
No fasta index found for ../bowtie-0.12.7/genomes/chr.fasta. Rebuilding, please wait..
Error: sequence lines in a FASTA record must have the same length!
[FAILED]
Error: could not execute cuffcompare
Traceback (most recent call last):
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 573, in ?
sys.exit(main())
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 556, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 406, in compare_meta_asm_against_ref
tmap = compare_to_reference(gtf_input_file, ref_gtf, fasta_file)
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 342, in compare_to_reference
exit(1)
TypeError: 'str' object is not callable
[Wed Sep 28 20:19:22 2011] Beginning transcriptome assembly merge
-------------------------------------------
[Wed Sep 28 20:19:22 2011] Preparing output location ./merged_asm/
[Wed Sep 28 20:19:22 2011] Converting GTF files to SAM
gtf_to_sam: /usr/lib64/libz.so.1: no version information available (required by gtf_to_sam)
[20:19:22] Loading reference annotation.
gtf_to_sam: /usr/lib64/libz.so.1: no version information available (required by gtf_to_sam)
[20:19:22] Loading reference annotation.
gtf_to_sam: /usr/lib64/libz.so.1: no version information available (required by gtf_to_sam)
[20:19:23] Loading reference annotation.
[Wed Sep 28 20:19:23 2011] Quantitating transcripts
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
You are using Cufflinks v1.1.0, which is the most recent release.
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_fileu98BBT doesn't appear to be a valid BAM file, trying SAM...
[20:19:23] Loading reference annotation.
[20:19:24] Inspecting reads and determining fragment length distribution.
Processed 4610 loci.
> Map Properties:
> Total Map Mass: 27713.00
> Read Type: 0bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[20:19:24] Assembling transcripts and estimating abundances.
Processed 4610 loci.
[Wed Sep 28 20:19:53 2011] Comparing against reference file xxx.gtf
You are using Cufflinks v1.1.0, which is the most recent release.
No fasta index found for ../bowtie-0.12.7/genomes/chr.fasta. Rebuilding, please wait..
Error: sequence lines in a FASTA record must have the same length!
[FAILED]
Error: could not execute cuffcompare
Traceback (most recent call last):
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 573, in ?
sys.exit(main())
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 556, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 406, in compare_meta_asm_against_ref
tmap = compare_to_reference(gtf_input_file, ref_gtf, fasta_file)
File "/home/student/yujinhai/cufflinks-1.1.0.Linux_x86_64/cuffmerge", line 342, in compare_to_reference
exit(1)
TypeError: 'str' object is not callable
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