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Old 11-03-2009, 10:44 AM   #1
axiom7
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Location: Southwest

Join Date: Aug 2009
Posts: 14
Default Samtools "is recognized as '*'" "truncated file" error

Hi,

I posted this last week to the samtools thread, but did not receive a reply, so I'm taking another stab at it:

samtools-0.1.6_x86_64-linux; precompiled version downloaded today

$ bowtie --version
bowtie version 0.11.3
64-bit
Built on myserver
Fri Oct 23 13:27:05 MDT 2009
Compiler: gcc version 4.1.2 20070115 (prerelease) (SUSE Linux)
Options: -O3
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

$ samtools faidx hs_ref_chr10.fa
$ cat hs_ref_chr10.fa.fai
gi|89161187|ref|NC_000010.9|NC_000010 135374737 105 70 71

Created sam format with bowtie in two ways (behavior described below is the same for both methods):
1. using -S in bowtie command
2. using samtools bowtie2sam.pl on a bowtie --refout map file

sam file from method 2 (chromosome 10 only):

$ cat ref00000.map.sam
@0-0-3-9833 0 gi|89161187|ref|NC_000010.9|NC_000010 62380535 0 15M * 0 0 GCAAAGGNNATCATT IIIIIIIIIIIIIII NM:i:1 X1:i:5 MD:Z:3A3N0N6
@0-0-3-9833 16 gi|89161187|ref|NC_000010.9|NC_000010 62382480 0 15M * 0 0 GGGCTANNGCTCATC IIIIIIIIIIIIIII NM:i:1 X1:i:5 MD:Z:7N0N6
@0-0-6-12817 0 gi|89161187|ref|NC_000010.9|NC_000010 6095909 0 15M * 0 0 TACCACCNNGCCCTT IIIIIIIIIIIIIII NM:i:1 X1:i:265 MD:Z:1A5N0N6
@0-0-6-12817 16 gi|89161187|ref|NC_000010.9|NC_000010 6097174 0 15M * 0 0 GCATCANNCTCCCGA IIIIIIIIIIIIIII NM:i:1 X1:i:265 MD:Z:7N0N6


$ samtools view -bt ~/work/hs_ref_chr/hs_ref_chr10.fa.fai -o out.bam ref00000.map.sam
[sam_header_read2] 1 sequences loaded.
[sam_read1] reference '16 gi|89161187|ref|NC_000010.9|NC_000010 6097174 0 15M * 0 0 GCATCANNCTCCCGA IIIIIIIIIIIIIII NM:i:1 X1:i:265MD:Z:7N0N6

' is recognized as '*'.
[main_samview] truncated file.

out.bam is created, but I cannot do anything further with it.
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