Fail to create index - Picardtools problem?

[duartemolha]

Hi

I tried to run the software (SECNVs 2.7.1) with this command:

python SECNVs.py -version -G Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa -T bins.bed -o output -e_tol 20 -f 5000 -min_len 150 -p 0.25 -nr 1000000 -rN none -eN gap -sc -pr -q 35 -ssr -n 2 -fs 180 -s 65 -sb -picard /home/user/anaconda3/envs/py27/bin/picard -GATK /home/user/anaconda3/envs/py27/bin/gatk -l 150

I am getting this error:

[SECNVs Fri Jul 8 12:39:12 2022] Error: Fail to create index (.dict) for the control.

since dict file are created by picard tools I assume this has something to do with it.

Can you help?

I have both picardtools and GATK installed on the path indicated and they work fine when called

I get fastq files but the software is croaking before producing BAM files.

Many thanks

Duarte