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nghiavtr / FuSeq

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Segmentation fault (core dumped) #22

Open pradyumnasagar opened 2 years ago

pradyumnasagar commented 2 years ago

I tried to run FuSeq on our RNASeq data ( single end, ion-torrent fastq files) with GRCh38 reference. after it starts it gives a warning saying [FuSeq] -- Use transcript-gene map for fitering fusion-equivalence classes and FuSeq stops saying Segmentation fault (core dumped)

The below is the full output of run

FuSeq -i TxIndexer_idx_k21 -l IU -1 /data/test/rnaseq.fastq -p 10 -g Homo_sapiens.GRCh38.107.gtf -o out_rna/

Logs will be written to out_rna/LogDir there is 0 lib [2022-08-17 16:04:35.421] [jointLog] [info] parsing read library format Loading 32-bit quasi index[2022-08-17 16:04:36.361] [stderrLog] [info] Loading Suffix Array [2022-08-17 16:04:36.361] [jointLog] [info] Loading Quasi index [2022-08-17 16:04:37.866] [stderrLog] [info] Loading Transcript Info [2022-08-17 16:04:38.263] [stderrLog] [info] Loading Rank-Select Bit Array [2022-08-17 16:04:38.391] [stderrLog] [info] There were 207877 set bits in the bit array [2022-08-17 16:04:38.447] [stderrLog] [info] Computing transcript lengths [2022-08-17 16:04:38.448] [stderrLog] [info] Waiting to finish loading hash Index contained 207877 targets [2022-08-17 16:04:43.238] [jointLog] [info] done [2022-08-17 16:04:43.238] [stderrLog] [info] Successfully loaded position hash [2022-08-17 16:04:43.238] [stderrLog] [info] Done loading index Loaded targets

[FuSeq] -- Use transcript-gene map for fitering fusion-equivalence classes

Segmentation fault (core dumped)

nghiavtr commented 2 years ago

Hi @pradyumnasagar,

Thank you for your interest in using FuSeq. Unfortunately, the current version of FuSeq can not work for single-end read fastq files.

Best, Nghia