Issue creating BAM index file

[munasur12]

Hi,

I am having issues creating index file for my BAM file. The error I am getting is : [E::hts_idx_push] unsorted positions. samtools index: "L003.trimmed_adapt_qual_PAIRED_results_sorted_fixmate_sorted.bam" is corrupted or unsorted

Here are the commands I am running:

1. maf-convert sam $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results.maf > $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results.sam 

2. samtools view -bt SWS484SPF_PBJ_ScaffoldsF500.fasta.fai $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results.sam > $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results.bam

3. samtools sort --reference SWS484SPF_PBJ_ScaffoldsF500.fasta -n $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results.bam -T $fprefix -O bam -o $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results_sorted.bam

4. samtools fixmate --reference SWS484SPF_PBJ_ScaffoldsF500.fasta $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results_sorted.bam -O bam $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results_sorted_fixmate.bam

5. samtools sort --reference SWS484SPF_PBJ_ScaffoldsF500.fasta -n $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results_sorted_fixmate.bam -T $fprefix -O bam -o $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results_sorted_fixmate_sorted.bam

6. samtools index $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results_sorted_fixmate_sorted.bam $indir/LAST/$fprefix.trimmed_adapt_qual_PAIRED_results_sorted_fixmate_sorted.bai

I am using LAST version 7.19 and samtools version 1.3. 

I would appreciate any insight you can give.

Thanks,

Muna

[munasur12]

Hi,

I have tried include the no header flag when running  maf-convert and the error still persists.

Any insight you can provide would be great.

Thanks,

Muna

[FrithMartin]

Hi:

I'm no sam-ology expert, just guessing here: maybe you need to remove "-n" from your final sort step, to get the needed sort order?

Have a nice day,

Martin Frith

---

From: last-...@googlegroups.com <last-...@googlegroups.com> on behalf of munasur12 <anuradha...@gmail.com>
Sent: Friday, March 4, 2016 12:59 AM
To: last-align
Subject: [last-align] Re: Issue creating BAM index file

 

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[geis...@gmail.com]

Op woensdag 2 maart 2016 20:58:25 UTC+1 schreef munasur12:

> Hi,
>
>
> I am having issues creating index file for my BAM file. The error I am getting is : [E::hts_idx_push] unsorted positions. samtools index: "L003.trimmed_adapt_qual_PAIRED_results_sorted_fixmate_sorted.bam" is corrupted or unsorted

> .......

would appreciate any insight you can give.
>
>
> Thanks,
> Muna

Dear Muna,
I'm having similar problems, from a maf file I cannot create a sam file, that I can converto to a bam file. Your second step, already fails in my case.
Did you get any answers, or have solved the issue?
Kidn regards,

Raymond

[Frith, Martin]

Hi Raymond,

could you tell us the exact error message (and what software versions you used)?

Have a nice day,

Martin Frith

https://sites.google.com/site/mcfrith/