Test data error: medaka stitch step file missing

[rhinempi]

Dear Developers,

I have encountered an error running test data on the Ont_R10 dataset. longread_umi nanopore_pipeline -d ont_r10_zymo_rrna.fq -o test_r10 -v 25 -q r10_min_high_g340 -m 3500 -M 6000 -s 90 -e 90 -f CAAGCAGAAGACGGCATACGAGAT -F AGRGTTYGATYMTGGCTCAG -r AATGATACGGCGACCACCGAGATC -R GACATCGAGGTGCCAAAC -c 2 -p 2 -t 10

Error message as follow:

[16:22:42] Read orientation filtering... [16:22:42] UMI match error filtering... [16:22:42] UMI bin/cluster size ratio filtering... [16:22:42] Print UMI matches... [16:22:42] Done.

Computers / CPU cores / Max jobs to run 1:local / 28 / 1 0

Computers / CPU cores / Max jobs to run 1:local / 28 / 10

Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete local:0/10/100%/0.0s local:0/1/100%/1.0s Computers / CPU cores / Max jobs to run 1:local / 28 / 1 local:0/1/100%/1.0s usage: medaka stitch [-h] [--debug | --quiet] [--regions REGIONS [REGIONS ...]] [--threads THREADS] [--no-fillgaps] inputs [inputs ...] draft output medaka stitch: error: the following arguments are required: output sed: can't read test_r10/raconx2_medakax1/consensus_raconx2_medakax1.fa: No such file or directory cat: test_r10/raconx2_medakax1/consensus_raconx2_medakax1.fa: No such file or directory

I have checked the scripts. I think the *_consensus.hdf files did not generate in the former step. But, I can't figure out why.

Thanks for the help. Liren

[rhinempi]

Oh, solved myself, thanks

[cstill3928]

Hi Liren,

I ran into a similar issue and was wondering how you went about fixing it?

Thanks, Chris

[rhinempi]

Hi Chris,

It is a bug in the pipeline. You need to edit one of the python scripts: longread-UMI-pipeline/scripts/polish_medaka.sh

Replace the section "# Stitch consensus sequences" to the following command:

# Stitch consensus sequences
medaka stitch \
  $OUT_DIR/consensus/*_consensus.hdf \
  $CONSENSUS_FILE \
  $OUT_DIR/consensus_${OUT_NAME}.fa

Best, Liren

[cstill3928]

Thanks Liren!