.fa is empty, index does not exist
algaebrown opened this issue · 4 comments
algaebrown commented
I had an error with CIRIquant. starting from Warning: Empty fasta file: '/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index.fa' then (ERR): "/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index" does not exist. I ran with 16 threads. CIRIerror.log is empty. Please help. Thanks
Full log:
[Fri 2022-05-27 17:20:13] [INFO ] Running CIRI2 for circRNA detection ..
[Fri May 27 17:20:14 2022] CIRI begins running
[Fri May 27 17:20:14 2022] Loading reference
[Fri May 27 17:20:47 2022] Requesting system to split SAM into 16 pieces
[Fri May 27 17:20:14 2022] CIRI begins running
[Fri May 27 17:20:14 2022] Loading reference
[Fri May 27 17:20:47 2022] Requesting system to split SAM into 16 pieces
Divided SAM sizes:
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samaa 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samab 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samac 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samad 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samae 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samaf 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samag 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samah 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samai 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samaj 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samak 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samal 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samam 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.saman 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samao 4395350130
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_unmapped.samap 4395350121
SAM was divided successfully.
First read of divided SAM files:
APO-1-R_unmapped.samab: A00475:448:HFLNKDRX2:1:2121:1081:20055
APO-1-R_unmapped.samac: A00475:448:HFLNKDRX2:1:2141:15637:24533
APO-1-R_unmapped.samad: A00475:448:HFLNKDRX2:1:2161:14235:34507
APO-1-R_unmapped.samae: A00475:448:HFLNKDRX2:1:2204:3106:5431
APO-1-R_unmapped.samaf: A00475:448:HFLNKDRX2:1:2223:16224:31125
APO-1-R_unmapped.samag: A00475:448:HFLNKDRX2:1:2243:20509:16626
APO-1-R_unmapped.samah: A00475:448:HFLNKDRX2:1:2262:8730:32424
APO-1-R_unmapped.samai: A00475:448:HFLNKDRX2:2:2104:7012:25848
APO-1-R_unmapped.samaj: A00475:448:HFLNKDRX2:2:2125:16559:12696
APO-1-R_unmapped.samak: A00475:448:HFLNKDRX2:2:2145:27679:10316
APO-1-R_unmapped.samal: A00475:448:HFLNKDRX2:2:2163:20998:27743
APO-1-R_unmapped.samam: A00475:448:HFLNKDRX2:2:2204:4562:18067
APO-1-R_unmapped.saman: A00475:448:HFLNKDRX2:2:2223:21305:14779
APO-1-R_unmapped.samao: A00475:448:HFLNKDRX2:2:2242:14931:8782
APO-1-R_unmapped.samap: A00475:448:HFLNKDRX2:2:2260:7943:23265
APO-1-R_unmapped.samaa: A00475:448:HFLNKDRX2:1:2101:1018:1000
First reads were recorded successfully.
[Fri May 27 17:39:25 2022] First scanning
[Fri May 27 17:39:25 2022] First scanning
Worker 1 begins to scan APO-1-R_unmapped.samal.
Worker 2 begins to scan APO-1-R_unmapped.samaj.
Worker 3 begins to scan APO-1-R_unmapped.samam.
Worker 4 begins to scan APO-1-R_unmapped.samad.
Worker 5 begins to scan APO-1-R_unmapped.samag.
Worker 6 begins to scan APO-1-R_unmapped.samaf.
Worker 7 begins to scan APO-1-R_unmapped.samai.
Worker 8 begins to scan APO-1-R_unmapped.samac.
Worker 9 begins to scan APO-1-R_unmapped.samah.
Worker 10 begins to scan APO-1-R_unmapped.samab.
Worker 11 begins to scan APO-1-R_unmapped.samak.
Worker 12 begins to scan APO-1-R_unmapped.samae.
[Fri 2022-05-27 17:41:16] [INFO ] Extract circular sequence
[Fri 2022-05-27 17:41:16] [INFO ] Building circular index ..
Settings:
Output files: "/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index.*.ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index.fa
Warning: Empty fasta file: '/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index.fa'
Warning: All fasta inputs were empty
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal HISAT2 exception (#1)
Command: hisat2-build --wrapper basic-0 -p 16 -f /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index.fa /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index
[Fri 2022-05-27 17:41:20] [INFO ] De novo alignment for circular RNAs ..
(ERR): "/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index" does not exist
Exiting now ...
Kevinzjy commented
Hi @algaebrown, it seems that you have probably run out of memory when running CIRI2. Please reduce the thread number and try again (similar to #31).