rr-hctg-track2 not found during polishing (fc_unzip.py)

[Neato-Nick]

Hi,

I'm running falcon_unzip.py on a ~70 Mb genome. Looks like the phasing step finished fine, but I errored out during polishing.

Digging into the stderr I found in 4-polish/track-reads, this is where the error starts. user_script.sh runs falconc rr-hctg-track2, but rr-hctg-track2 is not a valid command for falconc. Is it possible this tool wasn't shipped with the latest conda release?

falcon-unzip 1.3.5 falcon-kit 1.5.2 pypeflow 2.3.0

Running the pipeline on CentOS Linux release 7.2.1511 (Core)

[30403]finished run_tr_stage1('../../0-rawreads/build/raw_reads.db', /nfs2/hts/pacbio/jobs_root/001/001100/tasks/falcon_ns2.tasks.task_falcon0_dazzler_lamerge_apply_jobs...(126), 2500, 30)
# That writes a msgpack partial for each raw_reads.*.las file.
# Default n_core is n_cpu/2. TODO: Configure --n-core
# (We also use a proc for LA4Falcon, so this is half.)
# It is actually limited by number of files, but in theory we could use whole machine if we have enough blocks.

abs_rawread_to_contigs=$(readlink -f rawread_to_contigs) #TODO: No readlink
++ readlink -f rawread_to_contigs
+ abs_rawread_to_contigs=/dfs/BPP/Grunwald_Lab/home/carleson/genome_assembly/PacBio/ramorum/PR-18-069/4-polish/track-reads/rawread_to_contigs
cwd=$(pwd)
++ pwd
+ cwd=/dfs/BPP/Grunwald_Lab/home/carleson/genome_assembly/PacBio/ramorum/PR-18-069/4-polish/track-reads
cd ../..
+ cd ../..
falconc rr-hctg-track2 --read-to-contig-map=${cwd}/read_to_contig_map --output=${abs_rawread_to_contigs} --partials-fn=${cwd}/partials.json
+ falconc rr-hctg-track2 --read-to-contig-map=/abs/path/to/assembly/4-polish/track-reads/read_to_contig_map --output=/abs/path/to/assembly/4-polish/track-reads/rawread_to_contigs --partials-fn=/abs/path/to/assembly/4-polish/track-reads/partials.json
Unknown subcommand "rr-hctg-track2".  It is not similar to defined subcommands.