Sequence name doesnt match regex

[lailasa...@gmail.com]

Hi,

I have loaded my genome in IGV (same file as I used for read mapping), but when I want to load my bam files, I get the error message.

Error loading C:\Skrivbordet\ISP-D56-B_merge_sorted.bam: An error occurred while accessing: C:\Skrivbordet\ISP-D56-B_merge_sorted.bam

Error loading BAM file: htsjdk.samtools.SAMException: Sequence name 'gi|0|lcl|HPV-m16031680Anr.1|HumanPapillomavirusm16031680A(HPV-m16031680A),completegenome' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'  

I see that the name of the chromosome in the reference genome (gi|0|lcl|HPV-m16031680Anr.1|HumanPapillomavirusm16031680A(HPV-m16031680A),completegenome), and the name of the chromosome in the bam file are identical. 

I didnt have this problem before with an older version. Now I am using   v 2.7.2.

Any ideas how to solve this? Thanks.

[James Robinson]

This error is coming from the htsjdk, the library used to parse BAM files.  It looks like it is enforcing the rules on sequence (chromosome)names from the SAM/BAM specification,  section 1.4 here (RNAME): https://samtools.github.io/hts-specs/SAMv1.pdf

I suggest opening an issue here since any solution will involve the htsjdk team.  Let me know when that's done and I will comment and follow it.   Also, if you could post the first few lines of your fasta file that would be helpful.   

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/38a7c020-2f2a-4f3c-b004-c1edc9e482c9%40googlegroups.com.

[Helga Thorvaldsdottir]

Here's where you can file the htsjdk issue: https://github.com/samtools/htsjdk/issues 

[lailasa...@gmail.com]

Hi,

Now I have seem that the problem comes from the parenthesis I have in the naming of the chromosomes. This is the example of my fasta file:

>gi|0|lcl|HPV-mEV03c09nr.1|HumanPapillomavirus_mEV03c09(HPV-mEV03c09),completegenome

atggatttaaagacagtacaggatctcagaaaacatttacaggtacctacagaggacctgttggtagcttgtaatttttg

tggacactttttaacttttctagagcttcttgaatttgataataaaactttaaatcttatttggaaagaagggcatgctt

ttggatgttgctcacgctgtgcagcagcagtagctaaaatagaatttgagaatttttatgagaaaactgtaataggaaag

gaaatagaagctgagagtagaagtttgctttgttgtatagctgtaaggtgctgttactgtttaagatttttagattatct

agaaaagttgtatatttgctctcacaatttacaattttataaagtgagaggttgttggaaaggtgtttgcagacattgta

gacagatatgattgggaaagaagtaactataccagacattgagcttgagctgcaagaccttgtccagcccattgacctgc

attgtgacgaagtgctacctgaagagtcagaaaacctgtcagaatcttcacaagcagaggtggagcctgaaagaatcctc

ttcaagattgttgctccgtgtggaggctgtgaaacccgtctgaaaattcacatcgcgtctactcgttttggaattcgttg

cttggaagaattgttgctgtctgaactttgtttgctgtgtcctgtgtgcagaaatggcagacaatagaggtactgatcct

>gi|0|lcl|HPV-mEV03c104nr.1|HumanPapillomavirus_mEV03c104(HPV-mEV03c104),completegenome

atggctgcttattttcctcgtagtttagatgaatattgtaaatattttgagattgatttttttagtttacgactgcgttg

cattttttgtttattttatacaagctttgaggaccttgctgcttttcatactaagaaacttaatatagtttggagaagta

atgtaccttttgtatgctgtacaaaatgttgtagacattcagctttaatagagaaacagaaatactttcagtgctctgtc

aaatgcagaattttagatgctgttgttggtaaacctataactgaaatttatatgcggtgtacttggtgctttgcattact

ggattgtgctgaaaaagtagatttgtgtgccagagatgatttagcacttttaattcgtggctattggagagctgattgca

gaaactgctgcataaaagaatgagaggtcacgcaccagatataaaagacatagaattagattttcatgacttaattttac

cagcaaatgttcttgctccagaagagtcattgtcactagacgaagaaccagaggaggagccaaaagaaccttatagggtt

gacacctcttgtggagtttgcggaacaggtgtaaggattattgttatagccacttgtgcttcagtgcgtacagtgcagca

attacttttaagagaattgtcttttgtttgcgtcgagtgctacaggaccaggattcatcatgggggatcccagtaaaggt

actgataaaaatacttatgaaaacagtgaaagtgttgattggtttattgtgcatgaagctgactgtgtagatgatgactt

aaatgcgttagaaaatatatttgaagaaagcaacagtgatactgatatttcgaaccttatagacgatgatcaagtggatc

agggaaattccctggcactcttcaatactcagctagcaaatgattgtgagagagctttactagatctaaaacgaaagtat

attccaagccctgaaagatctattgcagatctgagtccgaggcttgctgctgtacatatttctccacaaagacaaatcaa

gaaaagattgtttgaggacagtggcgtagttgaagatgaagctgaaagtactaatgaaaatgtgcaggtagaaccaccac

gtgatagccgccatactgaaattcaaagtggtggtcaaataattgagttattaaaatgttctaactttaaagctttattt

ttagctaaatttaaagaactatttggggtttcgtaccatgatctgactagaacattcaaaagtgataaaacatgttgtga

I can easily remove it and rename the chromosomes for further analysis, but not sure if there is a turnaround to be able to see it in IGV for previous analyzed data. 

Thank you very much for the answer.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-...@googlegroups.com.

[katiev...@gmail.com]

Hi James, Helga, 

I have the same regex error (in my case it's due to a comma in the header e.g.  'gi|545903863|ref|NZ_BATA01000117.1|:1938-2201,2205-2258' and I've also seen it before with single quotes, as in 5' or 3'. I don't see an issue opened under htsjdk, did anyone come up with a solution or shall I open an issue?

Regards,

Katie.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-...@googlegroups.com.

[Laila Sara Arroyo Mühr]

I didn’t find a way to fix it but what I did is renaming my headers avoiding those “()” that gave me the issue, and it worked perfectly. Downside is that I had to redo the mapping...

Best

Sara

You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/8wRmwA-4skE/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/85d27c29-1e73-43fb-b069-0bc2ffa5adc2%40googlegroups.com.

--

Laila Sara Arroyo

[James Robinson]

Hi,

Does samtools load these bams?  If so I would suggest opening an issue in the htsjdk as they are inconsistent.   However if the sequence name is out of spec they might consider it a samtools problem, the htsjdk is stricter with respect to the spec.

If samtools can read the file you could fix the BAM without having to redo the alignments with a script,   bam -> sam -> rename script -> bam -> index

[Laila Sara Arroyo Mühr]

Hi,

Thanks for answering! I have worked with these files and Samtools to sort them, extracted only mapped reads, index, etc and it worked fine. The problem came when loading the reference in IGV.

Best

Sara

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/8wRmwA-4skE/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpvrWpjM16x7HEeG_dNXeA%2BfjTRLc91RfNW454V88XaA8A%40mail.gmail.com.

--

Laila Sara Arroyo

[lailasa...@gmail.com]

Great! Thanx!

[Katie Lennard]

Same here, samtools doesn't have a problem with the headers, only when trying to load to IGV.

On Tue, Apr 7, 2020 at 6:16 PM <lailasa...@gmail.com> wrote:

Great! Thanx!

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/8wRmwA-4skE/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/924d9970-244e-4f51-a78a-07c655ee0658%40googlegroups.com.

--

Katie

Bioinformatician

Division of Computational Biology
Institute of Infectious Diseases & Molecular Medicine
University of Cape Town

South Africa

+27 21 406 6176 

[Katie Lennard]

I have opened an issue here: https://github.com/samtools/htsjdk/issues/1471

[John Marshall]

On Tuesday, April 7, 2020, James Robinson wrote:

Does samtools load these bams?  If so I would suggest opening an issue in the htsjdk as they are inconsistent.   However if the sequence name is out of spec they might consider it a samtools problem, the htsjdk is stricter with respect to the spec.

Samtools does not in general enforce things like this when merely reading files, so would happily load the BAM files. Nonetheless it considers such sequence names out of spec and would likely complain or not find the expected sequence if you e.g. queried for regions in out-of-spec-named sequences in samtools view.

You can use this to your advantage to use the samtools reheader command to change the problematic characters directly in your BAM files (unless the records have SA tags or others that contain sequence names as text), or via samtools view -> SAM -> sed -> samtools view -> BAM as already suggested (which will also handle SA tags etc).

    John

[Katie Lennard]

Thanks John!

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/8wRmwA-4skE/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/7418e613-74e6-4161-b1ee-55eea6ee333d%40googlegroups.com.

[Laila Sara Arroyo Mühr]

Thanks! Very much appreciated. 

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/8wRmwA-4skE/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/7418e613-74e6-4161-b1ee-55eea6ee333d%40googlegroups.com.

--

Laila Sara Arroyo