limitSjdbInsertNsj error persists in Fusioncatcher/1.2

Hi Daniel,

I am using fusioncatcher/1.20 and still getting the same erro

Command that I used --->

fusioncatcher -p ${THREADS} --limitSjdbInsertNsj=3000000 --limitOutSJcollapsed=2000000 -d /data/CCRSB/apps/pipelineSnakes/pipeline-SB/conda/envs/fusion-catcher/share/fusioncatcher-1.20/db/current/ -i Xeno_September_22_2020_1.fastq.gz,XenoP0TCP5_Xeno_September_22_2020_2.fastq.gz -o ${LOCAL}

I still get the error . From STDERR file

Waiting for BLAT to finish running...
BLAT finished running.
Joining BLAT's output files...
Done.
Fixing PSL...
Sorting PSL...
Processing PSL...
Sorting again...
The end.

Fatal LIMIT error: the number of junctions to be inserted on the fly =1324998 is larger than the limitSjdbInsertNsj=1000000
Fatal LIMIT error: the number of junctions to be inserted on the fly =1324998 is larger than the limitSjdbInsertNsj=1000000
SOLUTION: re-run with at least --limitSjdbInsertNsj 1324998

From STDOUT file

ERROR: Workflow execution failed at step 429 while executing:
STAR
--runRNGseed 54321
--twopass1readsN -1
--twopassMode Basic
--genomeSAindexNbases 13
--sjdbOverhang 91
--alignIntronMax 1439093
--outFilterMatchNmin 16
--outFilterMatchNminOverLread 0.2667
--outFilterScoreMinOverLread 0.2667
--alignSplicedMateMapLminOverLmate 0.2667
--genomeDir /lscratch/15070682/gene-gene_split_star.fa.0_star/
--runThreadN 32
--seedSearchStartLmax 16
--alignSJoverhangMin 16
--alignSJstitchMismatchNmax 5 -1 5 5
--outSJfilterOverhangMin 10 10 10 10
--outSJfilterCountUniqueMin 1 1 1 1
--outSJfilterCountTotalMin 1 1 1 1
--outSJfilterDistToOtherSJmin 0 0 0 0
--outSJfilterIntronMaxVsReadN 1439093
1439093
1439093
--limitOutSAMoneReadBytes 100000000
--scoreGapNoncan -4
--scoreGapATAC -4
--readFilesIn /lscratch/15070682/reads_gene-gene_no-str_fixed.fq
--outFileNamePrefix /lscratch/15070682/gene-gene_split_star.fa.0_star-results/
Executing second time the same step/command in order to capture error messages (i.e. STDERR)...

Fatal LIMIT error: the number of junctions to be inserted on the fly =1324998 is larger than the limitSjdbInsertNsj=1000000

Can you please help ?

ndaniel / fusioncatcher

limitSjdbInsertNsj error persists in Fusioncatcher/1.2 #188