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cpouchon / ORTHOSKIM

ORTHOSKIM allows in silico capture of targeted sequences in genomic or transcriptomic libraries.
GNU General Public License v3.0
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Error during concatenation of alignments #13

Open andrzej-grz opened 1 year ago

andrzej-grz commented 1 year ago

Hi @cpouchon, I am trying to run test data in Orthoskim. I am following all steps according to provided tutorial. I have captured all sequences chloroplast_CDS, chloroplast_rRNA, chloroplast_tRNA, mitochondrion_CDS, mitochondrion_rRNA, nucrdna. Unfortunately for all captures, each time I am still facing the same issue during concatenation of alignments:

INFO: concatenation of alignments CMD: /home/keib/Documents/andrew/ORTHOSKIM-master/src/ConcatSeq.py -p /media/keib/data/andrew/Orthoskim/run_orthoskim/Alignment/alignments/ --pathfind -o /media/keib/data/andrew/Orthoskim/run_orthoskim/concatenated -t /home/keib/Documents/andrew/ORTHOSKIM-master/resources/selTaxa_Primulaceae.tab --missingfract 1 --target chloroplast_CDS,chloroplast_rRNA --clean -g /home/keib/Documents/andrew/ORTHOSKIM-master/resources/listGenes_To_Concat.tab Traceback (most recent call last): File "/home/keib/Documents/andrew/ORTHOSKIM-master/src/ConcatSeq.py", line 199, in Nratio=float(float(Ncount+gappcount)/float(SeqLength))


ZeroDivisionError: float division by zero

Thanks in advance,
Andrzej
cpouchon commented 1 year ago

Hi Andrzej, I think this is because the list of samples you used for the alignment was probably not correct. Here in the command the taxa that were used, the list of sample is: /home/keib/Documents/andrew/ORTHOSKIM-master/resources/selTaxa_Primulaceae.tab

You need to specify which taxa you want directly within the config file at: TAXA_ALN=~/ORTHOSKIM-master/resources/selTaxa_Primulaceae.tab

You can replace it by the /media/keib/data/andrew/Orthoskim/run_orthoskim/chloroplast_CDS_done.log file, for example: TAXA_ALN=/media/keib/data/andrew/Orthoskim/run_orthoskim/chloroplast_CDS_done.log

Let me know if it's ok, Cheers, Charles

andrzej-grz commented 1 year ago

Thank you! Yes, it works now. Sorry for quite obvious error. But, is it possible to combine in the final alignment sequences that have been captured with sequences I have used as a custom reference database? Thanks again! Best, Andrzej