Open Shirley-Q opened 5 years ago
Hi Opera Devs, I would like to join this issue since I got the same error like Shirley. I want to add some points: This error even occurs is you newly install opera and run it on the test dataset. The gab_filling.err file Shirley highlighted in her screenshot contained this error on my system:
/mnt/volume/projects/opera_test/OPERA-MS/test_files/..//OPERA-LG/bin//Remap.py /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.paf /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling_contig.fa > /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1_remap.out sh: 1: /mnt/volume/projects/opera_test/OPERA-MS/test_files/..//OPERA-LG/bin//Remap.py: not found
Best wishes, Felix
OPERA-MS.log gap_filling.err,log consensus_remapped_remapped.fasta.txt consensus.fa.txt first_tilling.coords.txt
Hi, I have got the similar errors. some opera_scaffolds do not in the [TILLING/consensus_remapped_remapped.fasta] and cause the error in gapfilling.pl line 219 & 211.
when I run it on the test dataset, I do not get any errors. Any help will be greatly apreciated. Best, JinQun Huang
Hi, I add an index '--no-gap-filling' and it worked.
Best wishes, Shirley
OPERA-MS.log gap_filling.err,log consensus_remapped_remapped.fasta.txt
Hi, I have got the similar errors. some opera_scaffolds do not in the [TILLING/consensus_remapped_remapped.fasta] and cause the error in gapfilling.pl line 219 & 211.
when I run it on the test dataset, I do not get any errors. Any help will be greatly apreciated. Best, JinQun Huang
Dear JinQun, Thank you for sharing those log files with us. I will need additional files to identify your problem:
Best,
Denis
Hi Opera Devs, I would like to join this issue since I got the same error like Shirley. I want to add some points: This error even occurs is you newly install opera and run it on the test dataset. The gab_filling.err file Shirley highlighted in her screenshot contained this error on my system:
/mnt/volume/projects/opera_test/OPERA-MS/test_files/..//OPERA-LG/bin//Remap.py /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.paf /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling_contig.fa > /mnt/volume/projects/opera_test/OPERA-MS/test_files/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1_remap.out sh: 1: /mnt/volume/projects/opera_test/OPERA-MS/test_files/..//OPERA-LG/bin//Remap.py: not found
Best wishes, Felix
Dear Felix, This not normal. Could you please check if the 'Remap.py' script is present in your installation directory ?
ls /mnt/volume/projects/opera_test/OPERA-MS/OPERA-LG/bin//Remap.py
If the file is not there, please download it directly from gitHub, and copy it in /mnt/volume/projects/opera_test/OPERA-MS/OPERA-LG/bin/
.
Best,
Denis
Hi, There is a gap filling error. What should I do? Thank you very much!
Best wishes, Shirley
Dear Shirley, Could you please run the following command to create the complete log file:
/home/emma/OPERA-MS/bin/get_log.sh /home/emma/QXJ/nanopore/AN1-cat5group_nannopore_RESULTS
And share the file OPERA-MS-LOG.tar.gz with us.
Best regards,
Denis
OPERA-MS.log gap_filling.err,log consensus_remapped_remapped.fasta.txt Hi, I have got the similar errors. some opera_scaffolds do not in the [TILLING/consensus_remapped_remapped.fasta] and cause the error in gapfilling.pl line 219 & 211. when I run it on the test dataset, I do not get any errors. Any help will be greatly apreciated. Best, JinQun Huang
Dear JinQun, Thank you for sharing those log files with us. I will need additional files to identify your problem:
- /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/0.Meta_MisAssemble/HLD/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.delta
- /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/0.Meta_MisAssemble/HLD/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa
Best,
Denis
Dear Denis, thank you for your reply. I can't find the [TILLING/first_tilling.delta], I think the [TILLING/first_tilling.coords] you may need.
Feel free to contact me if you need anything.
Best, JinQun Huang
OPERA-MS-LOG.tar.gz This is the OPERA-MS-LOG.tar.gz. Looking forward to your reply! Thanks! Best, Shirley
Dear Felix, This not normal. Could you please check if the 'Remap.py' script is present in your installation directory ?
ls /mnt/volume/projects/opera_test/OPERA-MS/OPERA-LG/bin//Remap.py
If the file is not there, please download it directly from gitHub, and copy it in
/mnt/volume/projects/opera_test/OPERA-MS/OPERA-LG/bin/
.Best,
Denis
Hi Denis, the file is present in the bin folder. I checked that but forgot to write it in my initial message. May it be better to open a new issue since we have basically 3 people with similar but not the same problems?
Best wishes, Felix
Dear Denis, OPERA-MS-LOG.tar.gz
This is the OPERA-MS-LOG.tar.gz. Looking forward to your reply! Thanks! Best, Shirley
OPERA-MS.log gap_filling.err,log consensus_remapped_remapped.fasta.txt Hi, I have got the similar errors. some opera_scaffolds do not in the [TILLING/consensus_remapped_remapped.fasta] and cause the error in gapfilling.pl line 219 & 211. when I run it on the test dataset, I do not get any errors. Any help will be greatly apreciated. Best, JinQun Huang
Dear JinQun, Thank you for sharing those log files with us. I will need additional files to identify your problem:
- /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/0.Meta_MisAssemble/HLD/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.delta
- /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/0.Meta_MisAssemble/HLD/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa
Best, Denis
Dear Denis, thank you for your reply. I can't find the [TILLING/first_tilling.delta], I think the [TILLING/first_tilling.coords] you may need.
Feel free to contact me if you need anything.
Best, JinQun Huang
Dear JinQun , Thank you for sharing the file with us. We just have pushed a new version of OPERA-MS that should solve your problem. Please clone the latest version.
Best regards,
--- Denis
Dear Felix, This not normal. Could you please check if the 'Remap.py' script is present in your installation directory ?
ls /mnt/volume/projects/opera_test/OPERA-MS/OPERA-LG/bin//Remap.py
If the file is not there, please download it directly from gitHub, and copy it in
/mnt/volume/projects/opera_test/OPERA-MS/OPERA-LG/bin/
. Best, DenisHi Denis, the file is present in the bin folder. I checked that but forgot to write it in my initial message. May it be better to open a new issue since we have basically 3 people with similar but not the same problems?
Best wishes, Felix
Hi Felix, I believe that you do not have a standard installation of python in your machine. We just have pushed a new version of OPERA-MS that should solve your problem. Please clone and try the latest version.
Best regards,
--- Denis
PS: Please create a new issue if the problem persist.
Dear Denis, I am so sorry. OPERA-MS-LOG.tar.gz
This is the new OPERA-MS-LOG.tar.gz. Looking forward to your reply! Thanks! Best, Shirley
OPERA-MS.log gap_filling.err,log consensus_remapped_remapped.fasta.txt Hi, I have got the similar errors. some opera_scaffolds do not in the [TILLING/consensus_remapped_remapped.fasta] and cause the error in gapfilling.pl line 219 & 211. when I run it on the test dataset, I do not get any errors. Any help will be greatly apreciated. Best, JinQun Huang
Dear JinQun, Thank you for sharing those log files with us. I will need additional files to identify your problem:
- /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/0.Meta_MisAssemble/HLD/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.delta
- /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/0.Meta_MisAssemble/HLD/RESULTS//intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa
Best, Denis
Dear Denis, thank you for your reply. I can't find the [TILLING/first_tilling.delta], I think the [TILLING/first_tilling.coords] you may need. Feel free to contact me if you need anything. Best, JinQun Huang consensus.fa.txt first_tilling.coords.txt
Dear JinQun , Thank you for sharing the file with us. We just have pushed a new version of OPERA-MS that should solve your problem. Please clone the latest version.
Best regards,
--- Denis
Dear Denis, Thank you for your improvement. I had cloned the last version(0.8.2) and installed the pipeline after your messages as above.
The commond run like this: perl /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/OPERA-MS/OPERA-MS.pl --short-read1 /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/METprrM_5MetaSample/HLD/1.Cleandata/HLD.IS270_Clean.1.fq.gz --short-read2 /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/METprrM_5MetaSample/HLD/1.Cleandata/HLD.IS270_Clean.2.fq.gz --long-read /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/METprrM_5MetaSample/HLD/1.Cleandata/HLD.filtered_subreads.fa --out-dir RESULTS --num-processors 16 But I get the same error(gap_filling.err) as before.
Furthermore, I notice the run.log get some error too. It seems that the file like RESULTS//intermediate_files/opera_long_read/GAPFILLING/opera_scaffold_462//POOL.fastq dose not exist.
Are there anything I can offer you to improvement this problem? Best, JinQun Huang
Dear JinQun,
Could you please run the following command to create the complete log file and send to us at tong_chengxuan@gis.a-star.edu.sg and bertrandd@gis.a-star.edu.sg:
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/OPERA-MS/bin/get_log.sh /zfssz3/BC_COM_P11/F16HTSNCKF1065/METmivM_HK/0.Meta_MisAssemble/HLD/RESULTS/
Best regards, Chengxuan
Dear chengxuan, Would you please have any advises to improve this issue? Thank you.
Best, JinQun Huang
Hi, I also got this error, even used test data. So I had to skip it by using --no-gap-filling. But I found a file racon.fa.err "/home/server/OPERA-MS/test_files/..//utils//racon: unrecognized option '--winlen'" Is there something whong with the version of racon? As racon v1.4.3 is used now not v0.5.0 which is listed in README
Dear Zoubinok, I am sorry for the late reply, I was in vacation during the past 3 weeks. As mentioned in the README, the racon version that should be used is v0.5.0. Did you had to install racon manually when you setup the dependencies ?
--- Denis
Hi, There is a gap filling error. What should I do? Thank you very much!
Best wishes, Shirley