index not built

[stfacc]

Running CIRIquant for circRNA quantification I obtain the error shown at the end of the attached log file.

It seems that the index is not built for some reason.
CAN_FCX.log

[Kevinzjy]

Hi @stfacc , could you show me the content in /data/kronos/sfacchini/rnaseq/circrna/CAN_FCX/circ/CAN_FCX_index.ciri and /data/kronos/sfacchini/rnaseq/circrna/CAN_FCX/CIRIerror.log ? It seems that CIRI2 failed to detect circRNAs from your data.

[stfacc]

CAN_FCX_index.ciri does not exist, there are instead CAN_FCX.ciri and CAN_FCX_index.fa: both files are empty.
CIRIerror.log is also empty.

I saw in the main log that the phase [Thu 2020-09-10 14:40:12] [INFO ] Extract circular sequence begins before all 64 threads completed the previous phase.

I tried reducing the number of threads to 16 and it worked fine.

[Kevinzjy]

Thanks for the feedback. By the way, running CIRI2 using multi-threads requires a large amounts of RAM, and we do not recommend to use more than 20 threads under any circumstances.

[algaebrown]

I experience a similar problem with 16 threads

[Fri 2022-05-27 18:36:29] [INFO ] Extract circular sequence
[Fri 2022-05-27 18:36:29] [INFO ] Building circular index ..
Settings:
  Output files: "/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-noD-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-noD-R_index.fa
Warning: Empty fasta file: '/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-noD-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-noD-R_index.fa /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-noD-R_index 
[Fri 2022-05-27 18:36:38] [INFO ] De novo alignment for circular RNAs ..
(ERR): "/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-noD-R_index" does not exist
Exiting now ...