RaxML error about wgfast

[jasonsahl]

I will try and catch this earlier. I think that it is actually a problem encountered before RAxML. Let me work on a solution. I might ask you for some test data so I can replicate the error

[jasonsahl]

Caroline,
Can you update the code and try again? I would also try to create a conda environment with the instructions provided and the corresponding version of RAxML.
thanks,
Jason

[CarolineOhrman]

I have updated the code and rerun wgfast. I still have the same problem. My dataset (reads) have 7 samples. I get the following output

LOG: 2019/11/25 14:09:52 - WG-FAST pipeline starting
LOG: 2019/11/25 14:09:52 - WG-FAST was invoked with the following parameters:
-m /home/carodl/projects/wgfast/reference/bestsnp.tsv \
-t /home/carodl/projects/wgfast/reference/nasp_raxml.tree \
-r /home/carodl/projects/wgfast/reference/reference.fasta \
-d ../fastq/ \
-x  /home/carodl/projects/wgfast/reference/nasp.PARAMS \
-p 2 \
-c 3 \
-o 0.9 \
-k F \
-s T \
-n 100 \
-g T \
-e /tmp \
-f 0.1 \
-y F \
-j ASC_GTRGAMMA \
-l 2
-------------------------
LOG: 2019/11/25 14:10:05 - Loop starting
coverage file is malformed
coverage file is malformed
number of SNPs in genome N6 =  14
number of discarded SNPs in genome N6 =  15
number of discarded Reference positions in genome N6 =  1
-------------------------
number of SNPs in genome N1 =  76
number of discarded SNPs in genome N1 =  3
number of discarded Reference positions in genome N1 =  0
-------------------------
coverage file is malformed
number of SNPs in genome N7 =  0
number of discarded SNPs in genome N7 =  0
number of discarded Reference positions in genome N7 =  0
-------------------------
sample %s had no calls and will not be inserted into the tree
number of SNPs in genome N3 =  84
number of discarded SNPs in genome N3 =  151
number of discarded Reference positions in genome N3 =  0
-------------------------
number of SNPs in genome N2 =  4656
number of discarded SNPs in genome N2 =  21
number of discarded Reference positions in genome N2 =  1
-------------------------
coverage file is malformed
coverage file is malformed
number of SNPs in genome N5 =  5
number of discarded SNPs in genome N5 =  0
number of discarded Reference positions in genome N5 =  0
-------------------------
number of SNPs in genome N4 =  0
number of discarded SNPs in genome N4 =  0
number of discarded Reference positions in genome N4 =  0
-------------------------
sample %s had no calls and will not be inserted into the tree
LOG: 2019/11/25 15:28:34 - number of callable positions in genome N4 = 0
LOG: 2019/11/25 15:28:34 - number of callable positions in genome N6 = 70
LOG: 2019/11/25 15:28:34 - number of callable positions in genome N1 = 108
LOG: 2019/11/25 15:28:34 - number of callable positions in genome N7 = 0
LOG: 2019/11/25 15:28:34 - number of callable positions in genome N2 = 4690
LOG: 2019/11/25 15:28:34 - number of callable positions in genome N5 = 5
LOG: 2019/11/25 15:28:34 - number of callable positions in genome N3 = 317
sed: can't read RAxML_labelledTree.out: No such file or directory
mv: cannot stat 'RAxML_labelledTree.out': No such file or directory
LOG: 2019/11/25 15:28:55 - error encountered running RAxML...check log file

In out.raxml.out I get this:

RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file

Fasta parsing error, RAxML expects an alignment.
the sequence before taxon >N3
: seems to have a different length

Thankyou for the help.

[jasonsahl]

Caroline,

Could you please update the code and try again? I did fix a problem where an insertion is called by GATK, which threw off the length of the alignment. I now check for this and mask the call. Thank you reporting the problem and hopefully this fixes it.

[CarolineOhrman]

Than you for updating. Will test as soon as I get a timeslot open in my schedule :)