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gSNAP aligner generating truncated sam file ?

Hi I tried to align almost more than 10 human genome datasets against the hg38. gsnap able to align, generating a truncated sam file. Can any way, suggest me how to sort it out ?

Command:

./gsnap -d hg38 -D /data/Likith/gmap-2018-05-30/share/hg38 -t 10 /data/shayantan/cancer_samples/sample1/fixed1_normal.fq  /data/shayantan/cancer_samples/sample1/fixed2_normal.fq  > S1.gsnap.sam

Input file sizes:

R1 & R2- 97Gb , 97 Gb
hg38 - 3.1 GB

output file:

S1.gsnap.sam - 410 GB

Viewing the sam file:

$ samtools view S1.testgsnap.sam | head
[W::sam_read1] Parse error at line 1
[main_samview] truncated file
assembly genome next-gen alignment
• 2,917 views • link
updated by h.mon h.mon • written by pinn pinn

Try just head S1.testgsnap.sam.

Also, are you sure you want all of the datasets merged together like this? Usually you want them as separate files.

• 1 views • link
written by Devon Ryan Devon Ryan

Hi, i'm able to view the SAM file with head that is not a problem. when converting from SAM to sort.bam its showing truncated sam file ? Is their any other way, can i convert to sort.bam ?

$ head S1.gsnap.sam 
>ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAGATCGGAAG  2 unpaired  CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJJIEHHHFFFEEDCEEDDDDDCDDDDDCDDDDCDCCCCCDBDB<   HSQ-700848:338:D168LACXX:1:2307:7299:80233
ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAccctaaccc   1..92   +chr5:11491..11582  start:0..end:9,matches:92,sub:0 segs:1,align_score:9,mapq:3 method:ext
ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAccctaaccc   1..92   -chr22:50807994..50807903   start:0..end:9,matches:92,sub:0 segs:1,align_score:9,mapq:3method:ext
<TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTAGATCGGAAG  1 unpaired  BC@FFFDDFHHHFGGGIJFHGHIJEHHIJJFHHIJJDFDGHIDHHIJJBFHHIJFHIIJHHHEHFFDFCEEE>B=BDD:AABDDABABDDCCBCDDDD?B>   HSQ-700848:338:D168LACXX:1:2307:7299:80233
TTAGGGTTAGGGTTAGGGTTAGGGTTAa-------------------------------------------------------------------------   1..27   -chr18:10187..10161 start:0..del:1,matches:27,sub:0 segs:3,align_score:8,mapq:40    method:ext-gmap
,---------------------------GGGTTAGGGTTAa-------------------------------------------------------------  28..39  -chr18:10159..10148 del:1..del:1,matches:12,sub:0
,---------------------------------------GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTAGggttaggg  40..93  -chr18:10146..10093 del:1..end:8,matches:54,sub:0

>CCCTAACCCTGACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAGATCGGAAGAG  1 unpaired  @@@BDEFFFH?DFADGGGGGEGHIGCEDDGHHGGIGIIGIFEGGGIIIIIGHIIIHIGI@ECEHHC@BEC@EEA=A=ABAAACCB<AACAC>@>8<?<9A<   HSQ-700848:338:D168LACXX:1:2111:5061:50207

Then with samtools:

samtools view -u S1.gsnap.sam | samtools sort -@ 20 -T /tmp/S1.gsnap.sam.sort -o  S1.gsnap.sam.sort.bam
[W::sam_read1] Parse error at line 1
[main_samview] truncated file.
• 1 views • link
updated by Devon Ryan Devon Ryan • written by pinn pinn

Ah, it's not actually writing a SAM file! Maybe there's an option to change that?

• 1 views • link
written by Devon Ryan Devon Ryan

1 answer

You have to specify sam as output format with -A sam or --format=sam.

  -A, --format=STRING            Another format type, other than default.
                                 Currently implemented: sam, m8 (BLAST tabular format)
• 1 views • link
written by h.mon h.mon

I'm able to view the output. Thanks

• 1 views • link
written by pinn pinn

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