Hi guys
I generated an alignment with bowtie asking for a sam format. Everything went nice and smooth and got the file paired_mapped.sam. After this I wanted to use the samtools package and therefore, after installing, the first thing I did was to use the samtools import command. After elaborating for a couple of hours I received the following error message:
<code>
sam_header_line_parse] expected '@XY', got [@ILLUMINA-C3C24B_0047:1:1:1052:1111#0 77 * 0 0 * *0 0 TTTATCTAATAAATGCATCCNTTCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACTACGGTTANC bbbbbbbbbbbcbbb`````Ebbbb`````bbbbbbabbbbbbbbbbbbbbbbbbba`bbcbbb`bb`b`BBBBB XM:i:0]
Hint: The header tags must be tab-separated.
[sam_header_read2] 33 sequences loaded.
<\code>
the first lines of my sam files are
[code]
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:23037639
@SQ SN:chr1_random LN:568933
@SQ SN:chr2 LN:18779844
@SQ SN:chr3 LN:19341862
@SQ SN:chr3_random LN:1220746
@SQ SN:chr4 LN:23867706
@SQ SN:chr4_random LN:76237
@SQ SN:chr5 LN:25021643
@SQ SN:chr5_random LN:421237
@SQ SN:chr6 LN:21508407
@SQ SN:chr7 LN:21026613
@SQ SN:chr7_random LN:1447032
@SQ SN:chr8 LN:22385789
@SQ SN:chr9 LN:23006712
@SQ SN:chr9_random LN:487831
@SQ SN:chr10 LN:18140952
@SQ SN:chr10_random LN:789605
@SQ SN:chr11 LN:19818926
@SQ SN:chr11_random LN:282498
@SQ SN:chr12 LN:22702307
@SQ SN:chr12_random LN:1566225
@SQ SN:chr13 LN:24396255
@SQ SN:chr13_random LN:3268264
@SQ SN:chr14 LN:30274277
@SQ SN:chr15 LN:20304914
@SQ SN:chr16 LN:22053297
@SQ SN:chr16_random LN:740079
@SQ SN:chr17 LN:17126926
@SQ SN:chr17_random LN:829735
@SQ SN:chr18 LN:29360087
@SQ SN:chr18_random LN:5170003
@SQ SN:chr19 LN:24021853
@SQ SN:chrUn LN:43154196
@PG ID:Bowtie VN:0.12.5 CL:"dir"
@ILLUMINA-C3C24B_0047:1:1:1052:1111#0 77 * 0 0 * * 0 0TTTATCTAATAAATGCATCCNTTCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACTACGGTTANC bbbbbbbbbbbcbbb`````Ebbbb`````bbbbbbabbbbbbbbbbbbbbbbbbba`bbcbbb`bb`b`BBBBB XM:i:0
[\code]
I do not understand what is going wrong, the field are separated by tabs.
Any idea please?
thanks a lot for your help
S
I generated an alignment with bowtie asking for a sam format. Everything went nice and smooth and got the file paired_mapped.sam. After this I wanted to use the samtools package and therefore, after installing, the first thing I did was to use the samtools import command. After elaborating for a couple of hours I received the following error message:
<code>
sam_header_line_parse] expected '@XY', got [@ILLUMINA-C3C24B_0047:1:1:1052:1111#0 77 * 0 0 * *0 0 TTTATCTAATAAATGCATCCNTTCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACTACGGTTANC bbbbbbbbbbbcbbb`````Ebbbb`````bbbbbbabbbbbbbbbbbbbbbbbbba`bbcbbb`bb`b`BBBBB XM:i:0]
Hint: The header tags must be tab-separated.
[sam_header_read2] 33 sequences loaded.
<\code>
the first lines of my sam files are
[code]
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:23037639
@SQ SN:chr1_random LN:568933
@SQ SN:chr2 LN:18779844
@SQ SN:chr3 LN:19341862
@SQ SN:chr3_random LN:1220746
@SQ SN:chr4 LN:23867706
@SQ SN:chr4_random LN:76237
@SQ SN:chr5 LN:25021643
@SQ SN:chr5_random LN:421237
@SQ SN:chr6 LN:21508407
@SQ SN:chr7 LN:21026613
@SQ SN:chr7_random LN:1447032
@SQ SN:chr8 LN:22385789
@SQ SN:chr9 LN:23006712
@SQ SN:chr9_random LN:487831
@SQ SN:chr10 LN:18140952
@SQ SN:chr10_random LN:789605
@SQ SN:chr11 LN:19818926
@SQ SN:chr11_random LN:282498
@SQ SN:chr12 LN:22702307
@SQ SN:chr12_random LN:1566225
@SQ SN:chr13 LN:24396255
@SQ SN:chr13_random LN:3268264
@SQ SN:chr14 LN:30274277
@SQ SN:chr15 LN:20304914
@SQ SN:chr16 LN:22053297
@SQ SN:chr16_random LN:740079
@SQ SN:chr17 LN:17126926
@SQ SN:chr17_random LN:829735
@SQ SN:chr18 LN:29360087
@SQ SN:chr18_random LN:5170003
@SQ SN:chr19 LN:24021853
@SQ SN:chrUn LN:43154196
@PG ID:Bowtie VN:0.12.5 CL:"dir"
@ILLUMINA-C3C24B_0047:1:1:1052:1111#0 77 * 0 0 * * 0 0TTTATCTAATAAATGCATCCNTTCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACTACGGTTANC bbbbbbbbbbbcbbb`````Ebbbb`````bbbbbbabbbbbbbbbbbbbbbbbbba`bbcbbb`bb`b`BBBBB XM:i:0
[\code]
I do not understand what is going wrong, the field are separated by tabs.
Any idea please?
thanks a lot for your help
S
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