ANGSD reference index error

[Beate Nurnberger]

Dear All,

I wonder whether the ANGSD users among you have come across the following error. I posted it on the github angsd issues page, but since there seems to be a bit of a backlog of open issues, perhaps I could pick your brains also.

Regards,

Beate

**********************************************************************

I seem to have the same problem that was raised and resolved in an earlier post (2014-07-29):

-> Problem with difference in zlib version used for compiling and linking
-> ZLIB_VERSION: 1.2.8 zlibversion: 1.2.11
-> angsd version: 0.920 (htslib: 1.6) build(Jan 17 2018 13:38:41)
-> Reading fasta: Bv_mixed_reference_masked_new.fasta
-> fai index file: 'Bv_mixed_reference_masked_new.fasta.fai' looks older than corresponding fastafile: 'Bv_mixed_reference_masked_new.fasta'.
-> Please reindex fasta file

This happens even though the index is created by the same shell script that calls angsd and shows up in my log file (via ls) prior to the angsd call. angsd commands that do not require a reference execute without error.

I realise that I am not using the latest version, but I don't spot any entries in the recent changelogs that seem to relate to this.

[Tim Booth]

Hi Beate,

I'm not a user of ANGSD but I have a couple of comments:

1) The version mismatch of ZLIB should not matter since it only differs in the minor version. I wouldn't worry about this.

2) The source for ANGSD shows that the check is made using aio::isNewer

Line 34 of https://github.com/ANGSD/angsd/blob/master/abcGetFasta.cpp

And this in turn uses a standard stat system call

Line 89 of https://github.com/ANGSD/angsd/blob/master/aio.cpp

I can't see much room for error in their code. I suspect that the timestamp on your .fasta.fai file really is somehow older than the .fasta file. Maybe some clock skew is involved? Can you use 'ls -l' or 'stat' in your shell script to see the mtimes on both files?

Cheers,

TIM

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[Beate Nurnberger]

Hi Tim,

Many thanks indeed for digging into the ANGSD code for this. The 2014 post suggested that the error message was wrongly printed when the .fai file could not be found. And this was fixed apparently.

This is what my log file says:

2021-06-16 15:55:46 ls /scratch/bdnurnberger/job_7866388.meta-pbs.metacentrum.cz
total 3488
-rw-rw---- 1 bdnurnberger fishery 3342920 Jun 16 15:55 Bv_mixed_reference_masked_new.fasta
-rw-rw---- 1 bdnurnberger fishery  217901 Jun 16 15:55 Bv_mixed_reference_masked_new.fasta.fai
-rw-rw---- 1 bdnurnberger fishery    2528 Jun 16 15:55 bamfiles_abs_path.txt
drwxrwx--- 2 bdnurnberger fishery       6 Jun 16 15:55 input
drwxrwx--- 2 bdnurnberger fishery       6 Jun 16 15:55 output
drwxrwx--- 2 bdnurnberger fishery       6 Jun 16 15:55 tmp
2021-06-16 15:55:46
2021-06-16 15:55:46  === running 'ANGSD...' ..
2021-06-16 15:55:46   .. done
2021-06-16 15:55:47 -- cleaning up --

It looks to me as if the timestamping is correct. I think I'll ask our sysadmin to install the latest version of angsd and then try again.

Regards,

Beate

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