HALC failed Unknown error 35072

[sagnikbanerjee15]

Hello,

I am trying to HALC to error correct long reads using contigs generated from short reads (using rnaSpades). I have converted the multiline fasta output of rnaSpades to single line contigs. The first two steps of the HALC run has finished successfully. The 3rd step fails and gives me the following error: "ERROR: Failed to run HALC:Unknown error 35072". Here is the complete error.

2018-12-21 22:02:40.540263

/////STEP 1 STARTED////////////////////////////////////////////////////////////////////////////////////////////////// Running command: Chunker -s 200M -o ./temp/step1/pb-%03d.fa /work/LAS/rpwise-lab/sagnik/PacBio_SBR/data/7-Dai_S1-ns_S4-ns_053017_40/A01_1/Analysis_Results/A01_1_fungal_subreads.fasta 1>./temp/step1/SeqChunker.out 2>./temp/step1/SeqChunker.err 2 files created

/////STEP 1 DONE/////////////////////////////////////////////////////////////////////////////////////////////////////

/////STEP 2 STARTED////////////////////////////////////////////////////////////////////////////////////////////////// Running command: blasr ./temp/step1/pb-001.fa /work/LAS/rpwise-lab/sagnik/PacBio_SBR/data/rnaspade_assembly/transcripts.fasta -m 5 --out ./temp/step2/blasrresult-001.m5 --maxScore 2000 --minMatch 8 --minAlnLength 15 --nCandidates 30 --bestn 20 --nproc 40 1>./temp/step2/blasr_1.out 2>./temp/step2/blasr_1.err Running command: blasr ./temp/step1/pb-002.fa /work/LAS/rpwise-lab/sagnik/PacBio_SBR/data/rnaspade_assembly/transcripts.fasta -m 5 --out ./temp/step2/blasrresult-002.m5 --maxScore 2000 --minMatch 8 --minAlnLength 15 --nCandidates 30 --bestn 20 --nproc 40 1>./temp/step2/blasr_2.out 2>./temp/step2/blasr_2.err

/////STEP 2 DONE/////////////////////////////////////////////////////////////////////////////////////////////////////

/////STEP 3 STARTED////////////////////////////////////////////////////////////////////////////////////////////////// Running command: HALC ./temp/step2/blasrresult-001.m5 /work/LAS/rpwise-lab/sagnik/PacBio_SBR/data/rnaspade_assembly/transcripts.fasta ./temp/step1/pb-001.fa -o ./temp/step3/ -p pb-001 -t 40 -b 4 -w 4 1>./temp/step3/HALC_1.out 2>./temp/step3/HALC_1.err ERROR: Failed to run HALC:Unknown error 35072

The HALC error file has this:

cat HALC_output_directory/temp/step3/HALC_1.err boundary = 4 coverage = auto width = 4 threads = 40 out = ./temp/step3/ prefix = pb-001 repeatfree = false

Making hashmap for long reads... Running time: 0h 0min 2s

Making hashmap for contigs... Running time: 0h 0min 1s

Reading map result... Running time: 0h 1min 5s

Preprocessing... Running time: 0h 41min 6s

Generating subcontigs... Running time: 0h 0min 2s

Building graph...

Please help.

Thank you.