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Oshlack / JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
https://github.com/Oshlack/JAFFA/wiki
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Error on running ONT data #93

Open parsboy66 opened 1 year ago

parsboy66 commented 1 year ago

Hi there, nice job!

i already install the tools and all steps perfectly installed , but running it on my own data or on the provided data(simulated one) im getting same error "terminate called after throwing an instance of 'std::regex_error' what(): Mismatched '[' and ']' in regular expression "

gcc i used is version 9.5 and the command i use is bpipe run ../../JAFFAL.groovy ../../LongReadFusionSimulation/ONT_fus_sim_75err.fastq.gz

i would be happy to get some help in order to solve the issue. Thanks

nadiadavidson commented 1 year ago

Thanks, I will have a look into this. Do you have a lower version of gcc you can try with a fresh installation? What type of system are you running on?

yuyun-zhang commented 6 months ago

Hi Nadia,

I meet the same issue when run JAFFAL version 2.3 in CentOS Linux release 7.9.2009:

${path}/tools/bin/bpipe run ${path}/JAFFAL.groovy LongReadFusionSimulation/ONT_fus_sim_75err.fastq.gz

I used simulated data that you provided.

Here is the log:

====================================================================================================
|                              Starting Pipeline at 2024-05-23 15:55                               |
====================================================================================================

========================================= Stage run_check ==========================================
Running JAFFA version 2.4_dev
Checking for required data files...
/u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38_genCode22.fa
/u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38_genCode22.tab
/u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/known_fusions.txt
/u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38.fa
/u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/Masked_hg38.1.bt2
/u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38_genCode22.1.bt2
All looking good

=============================== Stage get_fasta (ONT_fus_sim_75err) ================================
java -ea -Xmx200m -cp /u/project/gxxiao/gxxiao5/yuyun/software/JAFFA-version-2.3/tools/bbmap/current/ jgi.ReformatReads ignorebadquality=t in=LongReadFusionSimulation/ONT_fus_sim_75err.fastq.gz out=ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.fasta threads=16
Executing jgi.ReformatReads [ignorebadquality=t, in=LongReadFusionSimulation/ONT_fus_sim_75err.fastq.gz, out=ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.fasta, threads=16]
Set threads to 16
Input is being processed as unpaired
Input:                          17889 reads             38471166 bases
Output:                         17889 reads (100.00%)   38471166 bases (100.00%)
Time:                           1.295 seconds.
Reads Processed:       17889    13.81k reads/sec
Bases Processed:      38471k    29.71m bases/sec

========================= Stage minimap2_transcriptome (ONT_fus_sim_75err) =========================
[M::mm_idx_gen::8.658*1.53] collected minimizers
[M::mm_idx_gen::10.967*1.94] sorted minimizers
[M::main::10.967*1.94] loaded/built the index for 195175 target sequence(s)
[M::mm_mapopt_update::11.489*1.89] mid_occ = 110
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 195175
[M::mm_idx_stat::11.743*1.87] distinct minimizers: 16950829 (43.60% are singletons); average occurrences: 3.243; average spacing: 5.406
[M::worker_pipeline::30.983*4.24] mapped 17889 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: /u/project/gxxiao/gxxiao5/yuyun/software/JAFFA-version-2.3/tools/bin/minimap2 -t 16 -x map-ont -c /u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38_genCode22.fa ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.fasta
[M::main] Real time: 31.147 sec; CPU: 131.523 sec; Peak RSS: 2.459 GB

=========================== Stage filter_transcripts (ONT_fus_sim_75err) ===========================
Done reading in transcript IDs
Reading the input alignment file, ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.paf
terminate called after throwing an instance of 'std::regex_error'
  what():  Mismatched '[' and ']' in regular expression
bash: line 1: 13270 Aborted                 /u/project/gxxiao/gxxiao5/yuyun/software/JAFFA-version-2.3/tools/bin/process_transcriptome_align_table ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.paf 1000 /u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38_genCode22.tab > ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.txt
ERROR: Command failed with exit status = 134 : 

/u/project/gxxiao/gxxiao5/yuyun/software/JAFFA-version-2.3/tools/bin/process_transcriptome_align_table ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.paf 1000 /u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38_genCode22.tab > ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.txt 

========================================= Pipeline Failed ==========================================

One or more parallel stages aborted. The following messages were reported: 

Branch ONT_fus_sim_75err.fastq in stage Unknown reported message:

Command failed with exit status = 134 : 

/u/project/gxxiao/gxxiao5/yuyun/software/JAFFA-version-2.3/tools/bin/process_transcriptome_align_table ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.paf 1000 /u/home/y/yuyun/project-gxxiao5/software/JAFFA-version-2.3/hg38_genCode22.tab > ONT_fus_sim_75err.fastq/ONT_fus_sim_75err.fastq.txt

Use 'bpipe errors' to see output from failed commands.

gcc version:

gcc (GCC) 4.9.1
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

java version:

openjdk version "1.8.0_412"
OpenJDK Runtime Environment (Zulu 8.78.0.19-CA-linux64) (build 1.8.0_412-b08)
OpenJDK 64-Bit Server VM (Zulu 8.78.0.19-CA-linux64) (build 25.412-b08, mixed mode)

Could you please provide me with some advice on how to resolve this issue? Thank you!

Best, Yuyun

nadiadavidson commented 6 months ago

Hi @yuyun-zhang,

This looks like an issue we've seen before relates to the gcc version. However, we previously through that gcc 4.9.1 should be okay. Therefore can I ask you to check a couple of things:

Cheers, Nadia.

yuyun-zhang commented 6 months ago

Hi Nadia,

Thanks for the reply! It seems GCC 4.9.1 was not compatible with my process_transcriptome_align_table program. After reinstalling, the program is now working well for processing the simulated data. Thank you very much!

Best, Yuyun