sstacks Unable to parse catalog -Stacks v2.0 beta 10a

[two...@qq.com]

Hi there,

I have a problem when use denovo_map.pl , my command is " denovo_map.pl -m 3 -M ${num}  -n ${num} -T 16 --samples ${fq} -o stacks_M${num} --popmap popmap   --paired".

ustack and cstack  successed, but sstack aborted, and I found this error in denovomap.log:

"""

Searching for matches by sequence identity...

  Parsing stacks_M1/catalog.tags.tsv

  Parsing stacks_M1/catalog.snps.tsv

Error parsing stacks_M1/catalog.snps.tsv at line: 1. (8 fields).

Error: Unable to parse catalog, 'stacks_M1/catalog'

Aborted.

denovo_map.pl: Aborted because the last command failed (13)

"""

Then I check the catalog.snps.tsv file,it the first 10 lines look like this:

"""

# cstacks version 2.0Beta10a; catalog generated on 2018-04-21 16:22:20

1       104     E       0       T       C       -       -

3       84      E       0       G       A       -       -

3       120     E       0       T       A       -       -

4       31      E       0       G       T       -       -

4       103     E       0       G       A       -       -

4       147     E       0       A       C       N       -

5       10      E       0       C       T       -       -

5       18      E       0       A       G       -       -

7       143     E       0       T       G       -       -

"""

It seems the first column is locusID instead of sampleID, but my sample_*.snps.tsv looks normal as described in manual .so I wonder why this happened and what is the solution. I would  appreciate it  if anyone could help me.

Attachment are my logfile and popmap file.

gr

[Julian Catchen]

Hi gr,

For a short time period we removed one of the columns of the SNPs output
file when we were cleaning up these output files. However, we replaced
it to keep the SNP files uniform across ustacks/cstacks/sstacks. It
seems amongst the code churn you somehow got a version of the code where
this column is not being produced.

I would download the software again and rebuild it, it should work fine
with the current version. Also, I would recommend that you keep your
input data files zipped, so everything stays zipped as you run the
pipeline and your optimization routines. It will save you a lot of space
in the long run.

julian

[two...@qq.com]

Hi julian,

 

Thank for your reply.I downloaded the newest version(http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0Beta10a.tar.gz) and reinstalled  ,but I still stuck at sstacks(same error).I'm really confused now...

gr

在 2018年4月22日星期日 UTC+8下午10:33:10，Julian Catchen写道：

[JCAR]

Hi!

I found the same error running the denovo_map pipeline of the 2.0Beta10a version. Any help would be appreciated!

[Julian Catchen]

Right, sorry, you are correct, I missed it. There is a bug in this
release in writing the catalog SNPs file, but only if you are running
with unzipped files (the zipped/unzipped versions of the outputs are
written by different pieces of code). We don't routinely test the
pipeline with unzipped data, because we feel strongly you should keep
always keep your data files zipped.

To fix this, gzip the outputs from ustacks, then re-run ccstacks and
sstacks and all should work.

Alternatively, wait for our next release, which will be out shortly.

julian

two...@qq.com wrote:
> Hi julian,
> Thank for your reply.I downloaded the newest
> version(http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0Beta10a.tar.gz)
> and reinstalled ,but I still stuck at sstacks(same error).I'm really
> confused now...
>
> gr
>
> 在 2018年4月22日星期日 UTC+8下午10:33:10，Julian Catchen写道：
>
> Hi gr,
>
> For a short time period we removed one of the columns of the SNPs
> output
> file when we were cleaning up these output files. However, we replaced
> it to keep the SNP files uniform across ustacks/cstacks/sstacks. It
> seems amongst the code churn you somehow got a version of the code
> where
> this column is not being produced.
>
> I would download the software again and rebuild it, it should work fine
> with the current version. Also, I would recommend that you keep your
> input data files zipped, so everything stays zipped as you run the
> pipeline and your optimization routines. It will save you a lot of
> space
> in the long run.
>
> julian
>

> two...@qq.com <javascript:> wrote:
> > Hi there,
> >

> > I have a problem when use denovo_map.pl <http://denovo_map.pl> ,
> my command is " denovo_map.pl <http://denovo_map.pl>

> > -m 3 -M ${num} -n ${num} -T 16 --samples ${fq} -o stacks_M${num}
> > --popmap popmap --paired".
> > ustack and cstack successed, but sstack aborted, and I found this
> error
> > in denovomap.log:
> > """
> > Searching for matches by sequence identity...
> > Parsing stacks_M1/catalog.tags.tsv
> > Parsing stacks_M1/catalog.snps.tsv
> > Error parsing stacks_M1/catalog.snps.tsv at line: 1. (8 fields).
> > Error: Unable to parse catalog, 'stacks_M1/catalog'
> > Aborted.
> >

> > denovo_map.pl <http://denovo_map.pl>: Aborted because the last

[Lucy Tran]

Hi,

I've encountered a similar problem using Stacks v. 2.2. I ran the pipeline with the following command:

denovo_map.pl --samples [directory] --paired --popmap [population map file] -M 3 -n 2 -T 8 -X "ustacks:-d" -X "populations:-r 0.8" -X "populations:--write_single_snp" -X "populations:--hwe" -X "populations:--fst_correction bonferroni_win" -X "populations:--fstats" -X "populations:--fasta_loci" -X "populations:--vcf" -X "populations:--genepop" -X "populations:--structure" -X "populations:--phylip" -o [directory]

ustacks runs successfully, but then I receive an error at the cstacks stage.

From the denovo_map.log file:

cstacks
==========
/home/ltran20/stacks-2.2/bin/cstacks -P /scratch/ltran20/lizards/stacks_results_0.1 -M /scratch/ltran20/lizards/stacks_results_0.1/pop_JAR.txt -n 2 -p 8

cstacks parameters selected:
  Loci matched based on sequence identity.
  Number of mismatches allowed between stacks: 2
  Gapped alignments: enabled
Constructing catalog from 8 samples.

Initializing new catalog...
  Parsing /scratch/ltran20/lizards/stacks_results_0.1/JAR13_S4_L004_cutadapt_subset_corrected_len_56.tags.tsv.gz
Error parsing /scratch/ltran20/lizards/stacks_results_0.1/JAR13_S4_L004_cutadapt_subset_corrected_len_56.tags.tsv.gz at line: 2. (10 fields).
Error: Failed to initialize the catalog.

Is there a bug in the v. 2.2 release when writing the ustacks outputs?

Thanks,

Lucy

[Nicolas Rochette]

Hi Lucy,

No, this is a different issue. There may be an issue with the file itself (such as being truncated), or there may be no loci for this sample. It is hard to say anything more without seeing the complete denovo_map log file and the first lines of the problematic file.

Best,

Nicolas

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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