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gap filling error #30

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Shirley-Q opened this issue Aug 31, 2019 · 18 comments
Open

gap filling error #30

Shirley-Q opened this issue Aug 31, 2019 · 18 comments

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@Shirley-Q
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Hi,
There is a gap filling error. What should I do? Thank you very much!
gap

Best wishes,
Shirley
@FelixLanger
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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

@JinqunHuang
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JinqunHuang commented Sep 2, 2019 •
edited
Loading

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

@Shirley-Q
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Author

Hi,
I add an index '--no-gap-filling' and it worked.

Best wishes,
Shirley

@dbertran78
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Contributor

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

@dbertran78
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Contributor

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

@dbertran78
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Contributor

Hi,
There is a gap filling error. What should I do? Thank you very much!
gap

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

@JinqunHuang
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JinqunHuang commented Sep 2, 2019 •
edited
Loading

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

@Shirley-Q
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Author

OPERA-MS-LOG.tar.gz
This is the OPERA-MS-LOG.tar.gz. Looking forward to your reply! Thanks!
Best,
Shirley

@FelixLanger
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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

@Shirley-Q
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Dear Denis,
OPERA-MS-LOG.tar.gz

This is the OPERA-MS-LOG.tar.gz. Looking forward to your reply! Thanks!
Best,
Shirley

@dbertran78
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Contributor

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

@dbertran78
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Contributor

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

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.

@Shirley-Q
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Author

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

@JinqunHuang
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JinqunHuang commented Sep 5, 2019 •
edited
Loading

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.

run.log.txt

Are there anything I can offer you to improvement this problem?
Best,
JinQun Huang

@TongChengxuan
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Collaborator

Dear JinQun,

Could you please run the following command to create the complete log file and send to us at [email protected] and [email protected]:

/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

@JinqunHuang
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Dear chengxuan，
Would you please have any advises to improve this issue?
Thank you.

Best,
JinQun Huang

@zoubinok
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zoubinok commented Mar 1, 2020

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

@dbertran78
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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

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6 participants
@zoubinok @dbertran78 @Shirley-Q @TongChengxuan @FelixLanger @JinqunHuang