Two issue with obtaining strain bins

[xif033]

Hello,

I have encountered an error running "straintigs", and also have another question about the obtained strain bins. I am running the desmanflow on some samples. For the samples I was able to get a strain count estimation, I specified number of strain and ran the desmanflow again in order to obtain strain-specific contigs. My two issues are:

1. I was able to successfully get the strain bins for half of my samples, however, I noticed that most of the strains obtained is about only half of the size of the a regular E. coli genome - is it because the strain number specified is too high? Or we do not have enough depth and coverage to recover the genome? Do you have any suggestions?

2. For the other half of the samples, I ran into this errors while running straintigs:
   ERROR ~ Error executing process > 'straintigs'

Caused by:
Process straintigs terminated with an error exit status (1)

Command executed:

/home/xif033/tools/DESMAN//scripts/Lengths.py -i species.fa > species_contigs.bed
perl -p -i -e "s/ / 1 /g" species_contigs.bed

samtools faidx assembly.fa
for file in *.bam
do
bname=basename $file .bam
samtools index $file
samtools mpileup -l species_contigs.bed -f assembly.fa $file > $bname.pileup
done

/home/xif033/tools/DESMAN//scripts/pileups_to_freq_table.py assembly.fa *.pileup contigfreqs.csv
rm *.pileup
/home/xif033/tools/DESMAN//desman/Variant_Filter.py contigfreqs.csv -m 0.0 -v 0.03
/home/xif033/tools/DESMAN//scripts/CalcGeneCov.py contigfreqs.csv > contig_cov.csv

cut -f 1 elite.bed | sort | uniq > core_genes.txt
/home/xif033/tools/DESMAN//scripts/CalcDelta.py contig_cov.csv core_genes.txt cluster_core
/home/xif033/tools/DESMAN//bin/desman outputsel_var.csv -e outputtran_df.csv -o straincluster -r 1000 -i 100 -g 5
/home/xif033/tools/DESMAN//desman/GeneAssign.py cluster_coremean_sd_df.csv straincluster/Gamma_star.csv contig_cov.csv straincluster/Eta_star.csv -m 20 -v outputsel_var.csv -o straincluster -
-assign_tau > cluster.cout
/home/xif033/tools/DESMAN//scripts/write_strain_fasta.py species.fa straincluster_tau_star.csv strainclusteretaD_df.csv straincluster

Command exit status:
1

Command output:
(empty)

Command error:
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
Traceback (most recent call last):
File "/home/xif033/tools/DESMAN//scripts/pileups_to_freq_table.py", line 73, in
if ord(dd[5][bindex]) >= min_base_q:
IndexError: string index out of range

Work dir:
/oasis/scratch/comet/xif033/temp_project/HMP2/DESMAN/scripts/work/f6/2bcd625e3f706bd52121926064d43e

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option -resume

-- Check '.nextflow.log' file for details

Any input is appreciated!
Best,
Xin