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bioinfo-biols / CIRIquant

circular RNA quantification tools
https://sourceforge.net/projects/ciri/files/CIRIquant
MIT License
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Cannot split into 12 (16) pieces with size of 6246233965 and named them as /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-noD-R_unmapped.sam. Fatal error. Aborted. #37

Closed algaebrown closed 2 years ago

algaebrown commented 2 years ago

Hi I encounter this error when running CIRIquant -t 4 -1 output/fastqs/APO-1-R_1.Tr.fq.gz -2 output/fastqs/APO-1-R_2.Tr.fq.gz --config ciriconfig_full.yaml --library-type 2 -o output/ -p APO-1-R -t 12

log:

[Mon May 30 18:19:05 2022] Loading reference
[Mon May 30 18:19:39 2022] Requesting system to split SAM into 12 pieces
[Mon May 30 18:19:05 2022] CIRI begins running
[Mon May 30 18:19:05 2022] Loading reference
[Mon May 30 18:19:39 2022] Requesting system to split SAM into 12 pieces
 Divided SAM sizes:
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samaa         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samab         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samac         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samad         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samae         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samaf         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samag         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samah         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samai         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samaj         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samak         6136420186
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samal         6136420184
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samam         4602315006
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.saman         4602315423
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samao         4602315554
 /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.samap         4602314573
Cannot split /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.sam into 12 (16) pieces with size of 6136420186 and named them as /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.sam.
Fatal error. Aborted.
    please help, thanks. I am pretty suer I have write access to the output dir
Kevinzjy commented 2 years ago

Hi @algaebrown , the /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/HuR-1-R_unmapped.sama[m-p] seems to be the temporary files from your last run. Could you delete the output directory and run CIRIquant again?.

algaebrown commented 2 years ago

Got it. Thanks!!