"Use of uninitialized value" and "command not found" error while running OPERA-MS

[faye92sun]

I have installed the dependencies. My input is

perl ~/OPERA-MS/OPERA-MS.pl \
    --short-read1 ~/illumina/final_pure_reads_1.fastq \
    --short-read2 ~/illumina/final_pure_reads_2.fastq \
    --long-read /nanopore_reads/1/pass.fq \
    --no-ref-clustering \
    --num-processors 16 \
    --out-dir OPERA_MS_RESULTS_1 2> log.err

The output is

Use of uninitialized value $output_dir in substr at ~/OPERA-MS/OPERA-MS.pl line 236.
Use of uninitialized value $output_dir in concatenation (.) or string at ~/OPERA-MS/OPERA-MS.pl line 236.

mkdir -p /CURRENT_DIRECTORY//

OPERA-MS default database not found. You can download the default OPERA-MS-DB using the following command: perl OPERA-MS.pl install-db at /lomi_home/mengqi/OPERA-MS/OPERA-MS.pl line 67.

The log.err file says /var/spool/pbs/mom_priv/jobs/294013.mn01.SC: line 24: --no-ref-clustering: command not found

The config file says

ILLUMINA_READ_1 ~/illumina/final_pure_reads_1.fastq
ILLUMINA_READ_2 ~/illumina/final_pure_reads_2.fastq
LONG_READ /nanopore_reads/1/pass.fq
OUTPUT_DIR /CURRENT_DIRECTORY//
CONTIG_EDGE_LEN 80
CONTIG_WINDOW_LEN 340
CONTIG_LEN_THR 500
KMER_SIZE 60
LONG_READ_MAPPER blasr
SHORT_READ_ASSEMBLER megahit
NUM_PROCESSOR 2

I am not sure what the problem is. It worked fine on the test files, but not on my own files. Any help would be appreciated.

[jsgounot]

Hi Faye,

• Use of uninitialized value is a perl warning and not an error message.
• Your command not found is not an error from OPERA-MS but from your terminal, that somehow thinks that --no-ref-clustering is a new command line. Maybe an EOL character in your script?
• Your main problem is as stated in your output and described in the documentation: OPERA-MS default database not found. You can download the default OPERA-MS-DB using the following command: perl OPERA-MS.pl install-db.

Have a nice day, JS