Issue with barcode association in MPRAflow #79
Description
Hello
I'm having issues with barcode association pipeline in MPRA flow. The key the key error message in the log is:
46199 Floating point exception(core dumped) bwa index -a bwtsw design_rmIllegalChars.fa.
The full error log is
(MPRAflow) ubuntu@ip-10-0-1-119:~/repos/MPRAflow$ nextflow run association.nf --fastq-insert "Undetermined_S0_R1_001.fastq.gz" --fastq-insertPE "Undetermined_S0_R2_001.fastq.gz" --design "Tconv_design_edit.fa" --fastq-bc "Undetermined_S0_I1_001.fastq.gz" --name "test"
N E X T F L O W ~ version 20.01.0
Launching association.nf [spontaneous_engelbart] - revision: 087b40d39f
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MPRAflow v2.3.5"
Pipeline Name : MPRAflow
Pipeline Version: 2.3.5
Fastq insert : /home/ubuntu/repos/MPRAflow/Undetermined_S0_R1_001.fastq.gz
fastq paired : /home/ubuntu/repos/MPRAflow/Undetermined_S0_R2_001.fastq.gz
Fastq barcode : /home/ubuntu/repos/MPRAflow/Undetermined_S0_I1_001.fastq.gz
design fasta : /home/ubuntu/repos/MPRAflow/Tconv_design_edit.fa
minimum BC cov : 3
map quality : 30
base quality : 30
cigar string : n
min % mapped : 0.5
Output dir : outs
Run name : test
Working dir : /home/ubuntu/repos/MPRAflow/work
Container Engine: null
Current home : /home/ubuntu
Current user : ubuntu
Current path : /home/ubuntu/repos/MPRAflow
base directory : /home/ubuntu/repos/MPRAflow
Script dir : /home/ubuntu/repos/MPRAflow
Config Profile : standard
====================================================
Nextflow version 20.10 required! You are running v20.01.0.
Pipeline execution will continue, but things may break.
Please run nextflow self-update to update Nextflow.
executor > local (1)
executor > local (8)
[19/cd3696] process > count_bc_nolab [100%] 1 of 1 ✔
[19/1f5c3c] process > create_BWA_ref [ 0%] 0 of 1
[da/b1aacc] process > PE_merge [ 17%] 1 of 6
[- ] process > align_BWA_PE -
[- ] process > collect_chunks -
[- ] process > map_element_barcodes -
[- ] process > filter_barcodes -
Error executing process > 'create_BWA_ref (make ref)'
Caused by:
Missing output file(s) design_rmIllegalChars.fa.fai expected by process create_BWA_ref (make ref)
Command executed:
#!/bin/bash
bwa index -a bwtsw design_rmIllegalChars.fa
samtools faidx design_rmIllegalChars.fa
picard CreateSequenceDictionary REFERENCE=design_rmIllegalChars.fa OUTPUT=design_rmIllegalChars.fa".dict"
Command exit status:
0
Command output:
(empty)
Command error:
[bwa_index] Pack FASTA... 0.01 sec
[bwa_index] Construct BWT for the packed sequence...
executor > local (8)
[19/cd3696] process > count_bc_nolab [100%] 1 of 1 ✔
[19/1f5c3c] process > create_BWA_ref [100%] 1 of 1, failed: 1 ✘
[a3/a91f31] process > PE_merge [100%] 1 of 1
[- ] process > align_BWA_PE -
[- ] process > collect_chunks -
[- ] process > map_element_barcodes -
[- ] process > filter_barcodes -
WARN: Killing pending tasks (5)
Error executing process > 'create_BWA_ref (make ref)'
Caused by:
Missing output file(s) design_rmIllegalChars.fa.fai expected by process create_BWA_ref (make ref)
Command executed:
#!/bin/bash
bwa index -a bwtsw design_rmIllegalChars.fa
samtools faidx design_rmIllegalChars.fa
picard CreateSequenceDictionary REFERENCE=design_rmIllegalChars.fa OUTPUT=design_rmIllegalChars.fa".dict"
Command exit status:
0
Command output:
(empty)
Command error:
[bwa_index] Pack FASTA... 0.01 sec
[bwa_index] Construct BWT for the packed sequence...
.command.sh: line 2: 46199 Floating point exception(core dumped) bwa index -a bwtsw design_rmIllegalChars.fa
[faidx] Could not build fai index design_rmIllegalChars.fa.fai
INFO 2023-10-09 13:01:32 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
********** CreateSequenceDictionary -REFERENCE design_rmIllegalChars.fa -OUTPUT design_rmIllegalChars.fa.dict
13:01:32.546 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/ubuntu/repos/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/share/picard-2.20.8-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Oct 09 13:01:32 UTC 2023] CreateSequenceDictionary OUTPUT=design_rmIllegalChars.fa.dict REFERENCE=design_rmIllegalChars.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Oct 09 13:01:32 UTC 2023] Executing as ubuntu@ip-10-0-1-119 on Linux 5.15.0-1022-aws amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.20.8-SNAPSHOT
[Mon Oct 09 13:01:32 UTC 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=514850816
Work dir:
/home/ubuntu/repos/MPRAflow/work/19/1f5c3cabec72c8e26c068c5d00bed5
Any help would be much appreciated.