**Note: This has been resolved-- please see post 12 in this thread for the update.
Hello folks,
Nearly at my wits end with tophat. I've gone through this twice now, using Bowtie once and Bowtie2 once. After days of mapping reads and read segments, I get the error below when it comes to "Searching for junctions via segment mapping":
When I look at the segment_juncs log, I find out that the problem I have is that a single one of my segment BAM files lacks a header:
Does anyone have any suggestions as to how to deal with this? Considering that only a single one of the BAM files is missing a header, I'm hoping there is some way to repair it, using the same header found in all the other BAM files. Does anyone know if this is possible? I've tried using samtools reheader tool, but that for some odd reason sends what seems like millions of lines of weird symbols through my terminal (eventually crashing it) and doesn't end up changing the file at all.
Hello folks,
Nearly at my wits end with tophat. I've gone through this twice now, using Bowtie once and Bowtie2 once. After days of mapping reads and read segments, I get the error below when it comes to "Searching for junctions via segment mapping":
[2012-06-27 13:47:45] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2012-06-27 13:47:45] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-06-27 13:47:45] Checking for Samtools
Samtools version: 0.1.18.0
[2012-06-27 13:47:45] Checking for Bowtie index files
[2012-06-27 13:47:45] Checking for reference FASTA file
[2012-06-27 13:47:45] Generating SAM header for /work/jeremy/BowtieIndex/Mus_musculus/NCBI/build37.2/Sequence/Bowtie2Index/genome
format: fastq
quality scale: phred33 (default)
[2012-06-27 13:48:39] Preparing reads
left reads: min. length=40, max. length=100, 151335054 kept reads (1380 discarded)
right reads: min. length=40, max. length=100, 151333005 kept reads (3429 discarded)
[2012-06-27 16:54:38] Mapping left_kept_reads to genome genome with Bowtie2
[2012-06-28 10:53:22] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
[2012-06-28 16:06:36] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
[2012-06-28 20:40:10] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
[2012-06-29 02:13:31] Mapping left_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
[2012-06-29 07:53:33] Mapping right_kept_reads to genome genome with Bowtie2
[2012-06-30 02:23:29] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
[2012-06-30 07:03:59] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
[2012-06-30 12:44:20] Mapping right_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
[2012-06-30 17:33:54] Mapping right_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
[2012-06-30 23:10:44] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =1
[bam_header_read] invalid BAM binary header (this is not a BAM file).
-----------------------------------------------
[2012-06-27 13:47:45] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-06-27 13:47:45] Checking for Samtools
Samtools version: 0.1.18.0
[2012-06-27 13:47:45] Checking for Bowtie index files
[2012-06-27 13:47:45] Checking for reference FASTA file
[2012-06-27 13:47:45] Generating SAM header for /work/jeremy/BowtieIndex/Mus_musculus/NCBI/build37.2/Sequence/Bowtie2Index/genome
format: fastq
quality scale: phred33 (default)
[2012-06-27 13:48:39] Preparing reads
left reads: min. length=40, max. length=100, 151335054 kept reads (1380 discarded)
right reads: min. length=40, max. length=100, 151333005 kept reads (3429 discarded)
[2012-06-27 16:54:38] Mapping left_kept_reads to genome genome with Bowtie2
[2012-06-28 10:53:22] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
[2012-06-28 16:06:36] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
[2012-06-28 20:40:10] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
[2012-06-29 02:13:31] Mapping left_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
[2012-06-29 07:53:33] Mapping right_kept_reads to genome genome with Bowtie2
[2012-06-30 02:23:29] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
[2012-06-30 07:03:59] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
[2012-06-30 12:44:20] Mapping right_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
[2012-06-30 17:33:54] Mapping right_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
[2012-06-30 23:10:44] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =1
[bam_header_read] invalid BAM binary header (this is not a BAM file).
segment_juncs v2.0.3 (3443S)
---------------------------
[samopen] SAM header is present: 22 sequences.
Loading reference sequences...
Loading 10...done
Loading 11...done
Loading 12...done
Loading 13...done
Loading 14...done
Loading 15...done
Loading 16...done
Loading 17...done
Loading 18...done
Loading 19...done
Loading 1...done
Loading 2...done
Loading 3...done
Loading 4...done
Loading 5...done
Loading 6...done
Loading 7...done
Loading 8...done
Loading 9...done
Loading MT...done
Loading X...done
Loading Y...done
Loading ...done
>> Performing segment-search:
Loading left segment hits...
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
---------------------------
[samopen] SAM header is present: 22 sequences.
Loading reference sequences...
Loading 10...done
Loading 11...done
Loading 12...done
Loading 13...done
Loading 14...done
Loading 15...done
Loading 16...done
Loading 17...done
Loading 18...done
Loading 19...done
Loading 1...done
Loading 2...done
Loading 3...done
Loading 4...done
Loading 5...done
Loading 6...done
Loading 7...done
Loading 8...done
Loading 9...done
Loading MT...done
Loading X...done
Loading Y...done
Loading ...done
>> Performing segment-search:
Loading left segment hits...
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
Error: no SAM header found for file ./tophat_out/tmp/left_kept_reads_seg2.bam
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
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