How to rectify error while sorting the sam file

Question

[sunnykevin97]

HI I'm converting SAM to sort bam it showing SAM file is truncated. But when i view it using samtools it doesn't display truncated . Is their any other way to convert to bam SRR1.sam = 47 GB

Sorting bam

samtools view -u SRR1.sam | samtools sort -@ 5 -T /tmp/SRR1.samsort -o SRR1.sort.bam 
[W::sam_read1] Parse error at line 10363596
[main_samview] truncated file.
[bam_sort_core] merging from 5 files and 5 in-memory blocks...

[sunnykevin97]

**samtools view -bS SRR1.sam > SRR1.bam** 
[W::sam_read1] Parse error at line 10363596
[main_samview] truncated file.
SRR1.sam => 47 GB
SRR1.bam => 1.9 GB
samtools quickcheck -v -v -v -v SRR1.bam && echo 'all ok' 
verbosity set to 4
checking SRR1.bam
opened SRR1.bam
SRR1.bam is sequence data
SRR1.bam has 455 targets in header.
SRR1.bam has good EOF block.
all ok

[GenoMax]

sunnykevin97 : Please use ADD REPLY/ADD COMMENT when responding to existing answers/comments to keep threads logically organized.

SUBMIT ANSWER is for new answers to the original question.

[WouterDeCoster]

How did you obtain this sam file?

Answer 1

[lakhujanivijay]

first, just convert sam to bam

samtools view -bS your_file.sam > your_file.bam

Using samtools v 1.4.1

samtools quickcheck -v -v -v -v   your_file.bam && echo 'all ok'

Paste the output of your file

[GenoMax]

@Vijay: Samtools is now at v.1.9. You should upgrade.

[sunnykevin97]

I tried with samtools v.1.9 SRR.sam => 47 GB

samtools view -bS SRR.sam > SRR.bam 
[W::sam_read1] Parse error at line 10363596
[main_samview] truncated file.

SRR.bam => 1.9 GB
samtools quickcheck -v -v -v -v SRR.bam  && echo 'all ok' 
verbosity set to 4
checking SRR.bam
opened SRR.bam
SRR.bam is sequence data
SRR.bam has 455 targets in header.
SRR.bam has good EOF block.
all ok

[GenoMax]

There is something wrong with your file at that specified line.

Can you pull out lines around that error location: sed -n '10363595,10363597p;10363598q' your_file?

[sunnykevin97]

sed -n '10363595,10363597p;10363598q' SRR.sam

SRR.5228479 99  chr6    65895862    3   250M    =   65896126    513 TGGCCAATATGAAGGAGCTACTGGCTTCATGAAATTCCAAAATCCAGTGGGTCAGCAATTAAATCTTAAAGCTCCAAAATGACCTCCTTTGATTCCATGTCTCACACTTAGGCATGCTGATACAAGGGGTGGGCTCCCAAGGACTTGGGCAGCTCTGCCTCTGTGGCTCTTCAGGGTACATACCCCATGACTGCTTTCACAGGCTGGCATTGAGTGTCTGCTGTTTTTCCAAGTGCACAGTGCAAGCTGT  DDDDDIIIIIIIIIIGIIIIIIHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIHHIIIIIIIIIIGIIIIIIHIIIGHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIHHIIIIIIHIIIIHGIIIIIIIIIIIIIIIIIIIGIGIIGGGHHHHHGHEHHIIHFHIHHIIEHHGHIIIIHIHIICHEEC7FEHIHIGH?BAFEEHIHCHFGIHIIHHII?GIIH.  PQ:i:21 SM:i:3  UQ:i:0  MQ:i:0  XQ:i:0  NM:i:0
SRR.5228479 147 chr6    65896126    3   249M    =   65895862    -513    TTCTGGTGTATGGAGGATGGTGGCCATCTTCTCACAGCTCCACTAGGCACTGCCCCAATGGGCACTCAGTGTTGGGGCTCCAACCACACATTTCTCCTCTGTATTGCCCTAGTAGAGGTTTTCCATGAWarning - out of bounds at position (28,-1)
Warning - out of bounds at position (27,-1)

[GenoMax]

You could try to delete that problem record by doing: sed -i '10363596d' your.sam and see if that fixes the problem. Make a backup of the file (if you want to be careful) since the command will make the change in place. Otherwise you may need to re-do alignment.

[sunnykevin97]

I tried showing truncated sam file sed -i '10363596d' SRR.sam

samtools view -u SRR.sam | samtools sort -@ 10 -T test/SRR.sort -o SRR.bam

[W::sam_read1] Parse error at line 10363596 [main_samview] truncated file. [bam_sort_core] merging from 0 files and 10 in-memory blocks... Generated bam file - 1.8 GB

[GenoMax]

You may want to cut your losses and redo the alignment. Even if you manage to get past this error there may be something else wrong.