Open ArtyomVodnev opened 1 year ago
Hi Artyom, most likely your perl executable (/home/arvodnev/OPERA-MS/tools_opera_ms/perl
) is broken. You can try that: rm /home/arvodnev/OPERA-MS/tools_opera_ms/perl && ln -s $(which perl) /home/arvodnev/OPERA-MS/tools_opera_ms/perl
.
Thank you! The solution you suggested really helped!
Unfortunately, I got another error after some time after starting the program: `/home/arvodnev/OPERA-MS//tools_opera_ms/perl /home/arvodnev/OPERA-MS//OPERA-LG/bin//gapfilling.pl /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta /home/arvodnev/test_project/rawdata/LR/SRR23215007.fastq /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping 2 499 /home/arvodnev/OPERA-MS//OPERA-LG/bin/ /home/arvodnev/OPERA-MS//tools_opera_ms/ /home/arvodnev/OPERA-MS//tools_opera_ms/ /home/arvodnev/OPERA-MS//tools_opera_ms/ /home/arvodnev/OPERA-MS//tools_opera_ms//MUMmer3.23/ 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/gap_filling.err
Error in during gap_filling. Please see /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/gap_filling.err for details.`
The file content of gap_filling.err is: `/home/arvodnev/OPERA-MS//tools_opera_ms//perl /home/arvodnev/OPERA-MS//OPERA-LG/bin//extract_read_sequence.pl --edge-file /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping/edge_read_info.dat --contig-file /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta --opera-lr-dir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/../ --read-file /home/arvodnev/test_project/rawdata/LR/SRR23215007.fastq --output-directory /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/extract_read.err
cat /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/consensus_cmd.sh | xargs -L 1 -P 2 -I COMMAND sh -c "COMMAND" 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/consensus_cmd.sh.log
mkdir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING
rm /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa; for f in /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/operascaffold/racon.fa; do sed 's/Consensus_//' $f >> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa; done rm: cannot remove '/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa': No such file or directory
/home/arvodnev/OPERA-MS//tools_opera_ms//perl /home/arvodnev/OPERA-MS//OPERA-LG/bin//run_mummer_large_ref.pl /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.coords 2 /home/arvodnev/OPERA-MS//tools_opera_ms//MUMmer3.23/ > /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.out 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.err
Error during tilling generation. Please see /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.out and /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.err for details.`
The file content of tilling_1.err is: `rm -r /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF rm: cannot remove '/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY': No such file or directory rm: cannot remove '/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF': No such file or directory mkdir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF split /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa mkdir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY split /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta *** run the mummer mapping rm -r /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/mummer rm: cannot remove '/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/mummer': No such file or directory mkdir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/mummer cat /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/mummer/cmd_delta.txt | xargs -I cmd --max-procs=2 bash -c cmd > /dev/null
Error in during nucmer.`
The file content of tilling_1.out is empty.
I would be very grateful if you can advise what should be done to fix this error. Thank you again!
Hi,
your issue seems similar to #60 - Could you run one command line from the cmd_delta.txt
as mentioned in this thread?
I run one command line from the cmd_delta.txt
, but I got nothing
The command line I run is: /home/arvodnev/OPERA-MS//tools_opera_ms//MUMmer3.23//nucmer --nosimplify --maxmatch -p /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/mummer/split_3.fa_split_1.fa /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF/split_3.fa /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY/split_1.fa > /dev/null 2> /dev/null
In addition, the mummer
directory I found in GAPFILLING
, and not in TILLING
directory
/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/mummer
You have to remove the redirection in the command line: /home/arvodnev/OPERA-MS//tools_opera_ms//MUMmer3.23//nucmer --nosimplify --maxmatch -p /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/mummer/split_3.fa_split_1.fa /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF/split_3.fa /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY/split_1.fa
After removing the redirection, this is what I got:
ERROR: The following critical files could not be used /home/arvodnev/test_project/OPERA-MS/tools_opera_ms/MUMmer3.23/aux_bin/postnuc /home/arvodnev/test_project/OPERA-MS/tools_opera_ms/MUMmer3.23/aux_bin/prenuc /home/arvodnev/test_project/OPERA-MS/tools_opera_ms/MUMmer3.23/mgaps /home/arvodnev/test_project/OPERA-MS/tools_opera_ms/MUMmer3.23/mummer Check your paths and file permissions and try again
Did you move your OPERA-MS folder after installation? Anyway, you need to have a working nucmer for OPERA-MS to proceed. Maybe try to reinstall with your new location.
Yes, I moved it to the previous directory, after installation. That is, I need to uninstall and reinstall the program?
Hard to know for sure but that's definitely what you should try first.
Okay, thank you! I'll try and let you know if it helps.
Hello,
Unfortunately, after I reinstalled the program, I got the error again:
Error in during gap_filling. Please see /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/gap_filling.err for details.
the file content of gap_filling.err
is:
/home/arvodnev/OPERA-MS//tools_opera_ms//perl /home/arvodnev/OPERA-MS//OPERA-LG/bin//extract_read_sequence.pl --edge-file /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping/edge_read_info.dat --contig-file /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta --opera-lr-dir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/../ --read-file /home/arvodnev/test_project/rawdata/LR/SRR23215007.fastq --output-directory /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/extract_read.err
cat /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/consensus_cmd.sh | xargs -L 1 -P 2 -I COMMAND sh -c "COMMAND" 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/consensus_cmd.sh.log
mkdir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING
rm /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa; for f in /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/*opera_scaffold_*/racon.fa; do sed 's/Consensus_//' $f >> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa; done
rm: cannot remove '/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa': No such file or directory
/home/arvodnev/OPERA-MS//tools_opera_ms//perl /home/arvodnev/OPERA-MS//OPERA-LG/bin//run_mummer_large_ref.pl /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/REF /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/QUERY /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.coords 2 /home/arvodnev/OPERA-MS//tools_opera_ms//MUMmer3.23/ > /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.out 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.err
/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/..//scaffolds.scaf
/home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.coords
Gap length: 932742
Tiling length: 110761472 116456783
Fraction gap 0.00835085333963673
*** get_contig_and_corrected_read_in_gap /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.paf /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling_contig.fa
python /home/arvodnev/OPERA-MS//OPERA-LG/bin//Remap.py /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.paf /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling_contig.fa > /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1_remap.out
sh: 1: python: not found
Error during contig remapping. Please see /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1_remap.out for details.
the file content of tilling_1_remap.out
is empty.
Is there any other way to fix this?
Hi, it clearly says python is missing. Please try to resolve all your basic installation problems first.
Hello, I'm trying to run OPERA-MS using this command:
perl /home/arvodnev/OPERA-MS/OPERA-MS.pl --contig-file /home/arvodnev/test_project/AssembledSR/SPAdes/contigs.fasta --short-read1 /home/arvodnev/test_project/rawdata/SR/trimmed_1.fastq --short-read2 /home/arvodnev/test_project/rawdata/SR/trimmed_2.fastq --long-read /home/arvodnev/test_project/rawdata/LR/SRR23215007.fastq --out-dir /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY --long-read-mapper minimap2
And it stop running with error: `arvodnev@darwin ~/test_project $ ./HY.sh
mkdir -p /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY
version v0.9.0
[Thu Apr 20 11:37:04 2023] Short read assembly [1/9] [Thu Apr 20 11:37:04 2023] Skip [contig file provided as input]
rm -r /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly
mkdir -p /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly
[Thu Apr 20 11:37:06 2023] Long-read mapping and assembly graph generation [2/9]
rm -r /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping
mkdir -p /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping
/home/arvodnev/OPERA-MS//tools_opera_ms/perl /home/arvodnev/OPERA-MS//OPERA-LG/bin//OPERA-long-read.pl --contig-file /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/user_assembly/contigs.fasta --kmer 60 --long-read-file /home/arvodnev/test_project/rawdata/LR/SRR23215007.fastq --output-prefix opera --output-directory /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping --num-of-processors 2 --opera /home/arvodnev/OPERA-MS//OPERA-LG/bin/ --illumina-read1 /home/arvodnev/test_project/rawdata/SR/trimmed_1.fastq --illumina-read2 /home/arvodnev/test_project/rawdata/SR/trimmed_2.fastq --samtools-dir /home/arvodnev/OPERA-MS//tools_opera_ms/ --perl-dir /home/arvodnev/OPERA-MS//tools_opera_ms/ --minimap2 /home/arvodnev/OPERA-MS//tools_opera_ms/ --short-read-tooldir /home/arvodnev/OPERA-MS//tools_opera_ms/ --skip-opera 1 --skip-short-read-mapping 1 > /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping/OPERA-long-read.out 2> /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping/OPERA-long-read.err
Error in the long read processing. Please see log for details /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping/OPERA-long-read.out /home/arvodnev/test_project/AssemblyHY/OPERA-MS_HY/intermediate_files/read_mapping/OPERA-long-read.err. ` the file content of OPERA-long-read.err is: sh: 1: /home/arvodnev/OPERA-MS//tools_opera_ms/perl: not found
the file content of OPERA-long-read.out is empty
I will be glad if you can help me find a solution to this error. Thank you!