I just ran tophat2 on some data that I previously have alligned. It goes until the last step and I get an error and no output:
[2012-05-03 19:05:31] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-03 19:05:31] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-05-03 19:05:31] Checking for Samtools
Samtools version: 0.1.16.0
[2012-05-03 19:05:31] Checking for Bowtie index files
[2012-05-03 19:05:32] Checking for reference FASTA file
[2012-05-03 19:05:32] Generating SAM header for /scratch0/ref/hg19/bowtie/hg19
format: fastq
quality scale: phred33 (default)
[2012-05-03 19:06:04] Reading known junctions from GTF file
[2012-05-03 19:06:23] Preparing reads
left reads: min. length=100, count=28502086
right reads: min. length=100, count=28482455
[2012-05-03 19:33:03] Creating transcriptome data files..
[2012-05-03 19:34:30] Building Bowtie index from edited_igenome_Homo_Sapiens_GRCh37_genes.fa
[2012-05-03 20:16:30] Mapping left_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
[2012-05-03 21:23:04] Mapping right_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
[2012-05-03 22:29:54] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-05-03 22:53:32] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-05-03 23:17:06] Resuming TopHat pipeline with unmapped reads
[2012-05-03 23:17:58] Mapping left_kept_reads.m2g_um against hg19 with Bowtie2
[2012-05-03 23:44:12] Mapping left_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
[2012-05-03 23:49:55] Mapping left_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
[2012-05-03 23:55:08] Mapping left_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
[2012-05-04 00:01:12] Mapping left_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
[2012-05-04 00:07:12] Mapping right_kept_reads.m2g_um against hg19 with Bowtie2
[2012-05-04 00:33:45] Mapping right_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
[2012-05-04 00:39:45] Mapping right_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
[2012-05-04 00:46:05] Mapping right_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
[2012-05-04 00:52:44] Mapping right_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
[2012-05-04 00:58:14] Retrieving sequences for splices
[2012-05-04 01:01:41] Indexing splices
[2012-05-04 01:04:08] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
[2012-05-04 01:06:15] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
[2012-05-04 01:08:52] Mapping left_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
[2012-05-04 01:11:06] Mapping left_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
[2012-05-04 01:13:16] Joining segment hits
[2012-05-04 01:37:45] Mapping right_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
[2012-05-04 01:40:01] Mapping right_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
[2012-05-04 01:42:15] Mapping right_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
[2012-05-04 01:44:31] Mapping right_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
[2012-05-04 01:46:38] Joining segment hits
[2012-05-04 02:09:51] Reporting output tracks
Traceback (most recent call last):
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3774, in ?
sys.exit(main())
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3746, in main
params.gff_annotation)
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 2522, in compile_reports
os.rename(sorted_bam_parts[0], output_dir + "accepted_hits.bam")
IndexError: list index out of range
I ran on another dataset and the same thing happens.
This is the command I used:
tophat -G $GTF --no-novel-juncs --num-threads 8 -o $DSTDIR/output/tophat200/${BARCODE}_newGTF $REFERENCE $DSTDIR/reads/s_${LANE}_${BARCODE}_1.fastq $DSTDIR/reads/s_${LANE}_${BARCODE}_3.fastq
The only errors I see in the logs are:
reports.log
/share/apps/tophat-2.0.0.Linux_x86_64/tophat_reports: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory
long_spanning_reads.segs.log
/share/apps/tophat-2.0.0.Linux_x86_64/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory
These files do in fact exist.
Does any one else have this problem?
[2012-05-03 19:05:31] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-03 19:05:31] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-05-03 19:05:31] Checking for Samtools
Samtools version: 0.1.16.0
[2012-05-03 19:05:31] Checking for Bowtie index files
[2012-05-03 19:05:32] Checking for reference FASTA file
[2012-05-03 19:05:32] Generating SAM header for /scratch0/ref/hg19/bowtie/hg19
format: fastq
quality scale: phred33 (default)
[2012-05-03 19:06:04] Reading known junctions from GTF file
[2012-05-03 19:06:23] Preparing reads
left reads: min. length=100, count=28502086
right reads: min. length=100, count=28482455
[2012-05-03 19:33:03] Creating transcriptome data files..
[2012-05-03 19:34:30] Building Bowtie index from edited_igenome_Homo_Sapiens_GRCh37_genes.fa
[2012-05-03 20:16:30] Mapping left_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
[2012-05-03 21:23:04] Mapping right_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
[2012-05-03 22:29:54] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-05-03 22:53:32] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-05-03 23:17:06] Resuming TopHat pipeline with unmapped reads
[2012-05-03 23:17:58] Mapping left_kept_reads.m2g_um against hg19 with Bowtie2
[2012-05-03 23:44:12] Mapping left_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
[2012-05-03 23:49:55] Mapping left_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
[2012-05-03 23:55:08] Mapping left_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
[2012-05-04 00:01:12] Mapping left_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
[2012-05-04 00:07:12] Mapping right_kept_reads.m2g_um against hg19 with Bowtie2
[2012-05-04 00:33:45] Mapping right_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
[2012-05-04 00:39:45] Mapping right_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
[2012-05-04 00:46:05] Mapping right_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
[2012-05-04 00:52:44] Mapping right_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
[2012-05-04 00:58:14] Retrieving sequences for splices
[2012-05-04 01:01:41] Indexing splices
[2012-05-04 01:04:08] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
[2012-05-04 01:06:15] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
[2012-05-04 01:08:52] Mapping left_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
[2012-05-04 01:11:06] Mapping left_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
[2012-05-04 01:13:16] Joining segment hits
[2012-05-04 01:37:45] Mapping right_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
[2012-05-04 01:40:01] Mapping right_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
[2012-05-04 01:42:15] Mapping right_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
[2012-05-04 01:44:31] Mapping right_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
[2012-05-04 01:46:38] Joining segment hits
[2012-05-04 02:09:51] Reporting output tracks
Traceback (most recent call last):
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3774, in ?
sys.exit(main())
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3746, in main
params.gff_annotation)
File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 2522, in compile_reports
os.rename(sorted_bam_parts[0], output_dir + "accepted_hits.bam")
IndexError: list index out of range
I ran on another dataset and the same thing happens.
This is the command I used:
tophat -G $GTF --no-novel-juncs --num-threads 8 -o $DSTDIR/output/tophat200/${BARCODE}_newGTF $REFERENCE $DSTDIR/reads/s_${LANE}_${BARCODE}_1.fastq $DSTDIR/reads/s_${LANE}_${BARCODE}_3.fastq
The only errors I see in the logs are:
reports.log
/share/apps/tophat-2.0.0.Linux_x86_64/tophat_reports: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory
long_spanning_reads.segs.log
/share/apps/tophat-2.0.0.Linux_x86_64/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory
These files do in fact exist.
Does any one else have this problem?
Comment