tophat2 problem: No such file: left_kept_reads.m2g_um.candidates_and_unspl.bam

[tgenahmet]

I'm running into this problem while trying to get tophat2 to work. I'm running this on the test data that came with the software.

I did get an accepted_hits.bam but it only contains the header.

[2012-04-13 12:12:14] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-04-13 12:12:14] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-04-13 12:12:14] Checking for Samtools
Samtools version: 0.1.18.0
[2012-04-13 12:12:14] Checking for Bowtie index files
[2012-04-13 12:12:14] Checking for Bowtie index files
[2012-04-13 12:12:14] Checking for reference FASTA file
[2012-04-13 12:12:14] Generating SAM header for /scratch/akurdogl/tophatForB37/Homo_sapiens.GRCh37.62
format: fastq
quality scale: phred33 (default)
[2012-04-13 12:12:33] Reading known junctions from GTF file
[2012-04-13 12:12:51] Preparing reads
left reads: min. length=75, count=100
right reads: min. length=75, count=100
[2012-04-13 12:12:51] Using pre-built transcriptome index..
[2012-04-13 12:13:30] Mapping left_kept_reads against transcriptome ensembl.63.genes with Bowtie2
[2012-04-13 12:14:03] Mapping right_kept_reads against transcriptome ensembl.63.genes with Bowtie2
[2012-04-13 12:14:36] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-04-13 12:14:51] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-04-13 12:15:05] Resuming TopHat pipeline with unmapped reads
[2012-04-13 12:15:05] Mapping left_kept_reads.m2g_um against Homo_sapiens.GRCh37.62 with Bowtie2
[2012-04-13 12:15:10] Mapping left_kept_reads.m2g_um_seg1 against Homo_sapiens.GRCh37.62 with Bowtie2 (1/3)
[2012-04-13 12:15:13] Mapping left_kept_reads.m2g_um_seg2 against Homo_sapiens.GRCh37.62 with Bowtie2 (2/3)
[2012-04-13 12:15:17] Mapping left_kept_reads.m2g_um_seg3 against Homo_sapiens.GRCh37.62 with Bowtie2 (3/3)
[2012-04-13 12:15:21] Mapping right_kept_reads.m2g_um against Homo_sapiens.GRCh37.62 with Bowtie2
[2012-04-13 12:15:25] Mapping right_kept_reads.m2g_um_seg1 against Homo_sapiens.GRCh37.62 with Bowtie2 (1/3)
[2012-04-13 12:15:28] Mapping right_kept_reads.m2g_um_seg2 against Homo_sapiens.GRCh37.62 with Bowtie2 (2/3)
[2012-04-13 12:15:32] Mapping right_kept_reads.m2g_um_seg3 against Homo_sapiens.GRCh37.62 with Bowtie2 (3/3)
[2012-04-13 12:15:36] Searching for junctions via segment mapping
[2012-04-13 12:17:53] Retrieving sequences for splices
[2012-04-13 12:20:18] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
[2012-04-13 12:22:06] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/3)
[2012-04-13 12:23:18] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/3)
[2012-04-13 12:24:29] Mapping left_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/3)
[2012-04-13 12:25:39] Joining segment hits
[2012-04-13 12:27:55] Mapping right_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/3)
[2012-04-13 12:29:08] Mapping right_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/3)
[2012-04-13 12:30:19] Mapping right_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/3)
[2012-04-13 12:31:30] Joining segment hits
[2012-04-13 12:33:46] Reporting output tracks
Traceback (most recent call last):
File "/home/akurdogl/bin/tophat2/bin/tophat", line 3778, in ?
sys.exit(main())
File "/home/akurdogl/bin/tophat2/bin/tophat", line 3754, in main
os.remove(m)
OSError: [Errno 2] No such file or directory: '/scratch/akurdogl/tophatTest/test_data/ref37test//tmp/left_kept_reads.m2g_um.candidates_and_unspl.bam'

[Jon_Keats]

Check site tophat site for updated version of tophat2, same version number but different. Is the test set really only 100 reads? Might be insufficient?

[townway]

I have similar errors,

[2012-05-24 16:47:41] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':Loading insertions...Error: malformed insertion coordinate record

Originally Posted by Jon_Keats

Check site tophat site for updated version of tophat2, same version number but different. Is the test set really only 100 reads? Might be insufficient?