why i cant have sam, sorted bam or bed by tophat output?
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0
Entering edit mode
6.1 years ago
A ★ 4.0k

hi friends,

my results with below syntaxes:

$TOP/tophat2 --no-coverage-search --no-convert-bam --b2-sensitive --b2-D 20 --b2-R 3 --b2-N 0 --b2-L 20 --read-gap-length 12 --read-mismatches 2 --read-edit-dist 13 --max-insertion-length 20 --max-deletion-length 30 -p 8 -G genes.gtf genome SRR1944914_trimmed_unmapped.fastq

resulting in:

[2015-09-04 09:36:52] Reporting output tracks
    [FAILED]
Error running:
/usr/data/nfs6/izadi/test/tophat-2.1.0.Linux_x86_64/samtools_0.1.18 merge -f -h ./tophat_out/tmp/genome_genome.bwt.samheader.sam -u - ./tophat_out/tmp/accepted_hits0_sorted.bam ./tophat_out/tmp/accepted_hits1_sorted.bam ./tophat_out/tmp/accepted_hits2_sorted.bam ./tophat_out/tmp/accepted_hits3_sorted.bam ./tophat_out/tmp/accepted_hits4_sorted.bam ./tophat_out/tmp/accepted_hits5_sorted.bam ./tophat_out/tmp/accepted_hits6_sorted.bam ./tophat_out/tmp/accepted_hits7_sorted.bam | /usr/data/nfs6/izadi/test/tophat-2.1.0.Linux_x86_64/samtools_0.1.18 view -h -

<p>[izadi@lbox161 bowtie2-2.2.5]$ $TOP/tophat2 --no-coverage-search --no-sort-bam --b2-sensitive --b2-D 20 --b2-R 3 --b2-N 0 --b2-L 20 --read-gap-length 12 --read-mismatches 2 --read-edit-dist 13 --max-insertion-length 20 --max-deletion-length 30 -p 8 -G genes.gtf genome SRR1944914_trimmed_unmapped.fastq[2015-09-04 09:52:18] Reporting output tracks<br />
<strong>[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_0.bam&quot;.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_1.bam&quot;.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_2.bam&quot;.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_3.bam&quot;.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_4.bam&quot;.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_5.bam&quot;.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_6.bam&quot;.
[bam_header_read] bgzf_check_EOF: Invalid argument
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from &quot;./tophat_out/tmp/unmapped_left_7.bam&quot;.
-----------------------------------------------
[2015-09-04 09:54:10] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2015-09-04 09:54:10] Run complete: 00:06:48 elapsed

when i tried to have a sam output, produced sam was empty...when i tried to have unsorted bam, i got error...
how i can have a valid sam please because when i tried to sort accepted_hit.bam i got error...
what is the fault please

tophat bam • 2.5k views
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0
Entering edit mode
6.1 years ago

It seems your SAM / BAM files have not the header

See this thread and also this one to learn how to add it

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