Malabady

Thanks! here is it reads_to_ctg_map.py --threads 2 \ /home/malabady/Projects/Ab10/Ab10Only_reads/reads/passQC_corr/mp6k75_good_1.cor.fastq.gz \ /home/malabady/Projects/Ab10/Ab10Only_reads/reads/passQC_corr/mp6k75_good_2.cor.fastq.gz \ /home/malabady/Projects/Ab10/Ab10Only_reads/assembly/spades/scaffolds.min0.5k.fasta \ mp6k75.bwa.bam \

theres is no back slash are the end of the last line.

Just got a clone of BESST using git clone and rerun the script again but it produced the same error (see below.) earlier I was looking up this error online...

But mp6k75.bwa.bam dir is generated by the script during the run. I didn't make it. I think the script the need to be modified not to produce this folder!!

this part: pysam.sort("-o", bwa_output + ".bam", output_path)

Hi @jacquelinemattos Here is my gene.txt file: ``` GSTU13,Arabidopsis_thaliana,https://www.uniprot.org/uniprotkb/Q9FUS6.fasta Q3ECW8,Arabidopsis_thaliana,https://www.uniprot.org/uniprotkb/Q3ECW8.fasta A0A1L7NZV0,Sarracenia_purpurea,https://www.uniprot.org/uniprotkb/A0A1L7NZV0.fasta A0A1L7NZV4,Sarracenia_purpurea,https://www.uniprot.org/uniprotkb/A0A1L7NZV4.fasta A0A1L7NZU7,Sarracenia_purpurea,https://www.uniprot.org/uniprotkb/A0A1L7NZU7.fasta ```` if you are using NCBI links, test the links first with wget. Good luck.

Hi @jacquelinemattos Your NCBI links are pointing to the HTML report page, not the plain fasta file. so, the workflow is not able to access the sequencing. I suggest using...

sorry, the link to the citrus gene is: https://rest.uniprot.org/uniparc/UPI0003D74F46.fasta

Hello, Thank you for the replies. As you suspected, there was a failure in parsing the "comparison" file because all single species lines had an extra tab at the end...

Hi @jeffersonfparil Just want to report that I am getting the same error message as well. I don't see the file ``ORTHOGROUPS_SINGLE_GENE.NT.timetree.nex`` in the output folder. I checked `bc` and...