Assembly_reads fails with IOError

ClaudiaPaetzold commented 5 years ago

I am trying to assemble our cleaned reads using the assemble-reads function and run into the following error:

`>(secapr_env) sysbot@ug-ubgb900-c119:/media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/trimmed$ secapr assemble_reads --input /media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/trimmed/ --output /media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/assembled/

################################################## Processing sample Zcori Traceback (most recent call last): File "/usr/local/anaconda3/envs/secapr_env/bin/secapr", line 6, in sys.exit(secapr.main.main()) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/main.py", line 50, in main args.func(args) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/assemble_reads.py", line 146, in main contig_count_df = get_stats_abyss(sample_output_folder,sample_id,sample_contig_count_dict) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/assemble_reads.py", line 251, in get_stats_abyss contig_count = count_contigs(contig_file) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/assemble_reads.py", line 245, in count_contigs return sum([1 for line in open(contig, 'rU').readlines() if line.startswith('>')]) IOError: [Errno 2] No such file or directory: '/media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/assembled/Zcori.fa'

Secpar (including abyss) was installed via conda on a Ubuntu 14.04 system. Also in the function there is no option to specify the --assembler parameter. Could there be some error in the installation? If not could you please help me identify the problem? Thank you.

tandermann commented 5 years ago

It might be that you somehow installed an outdated version of the software. What response do you get when you type ’secapr —version’?

Tobias Andermann (Hofmann) PhD student Biological and Environmental Sciences, University of Gothenburg The Antonelli Lab http://antonelli-lab.net/ | Gothenburg Global Biodiversity Centre http://ggbc.gu.se/ Carl Skottsbergs gata 22 B https://goo.gl/maps/mwGPq3HNzAN2, 413 19 Göteborg tobias.andermann@bioenv.gu.se mailto:tobias.andermann@bioenv.gu.se +46 76 090 1106 github.com/tobiashofmann88 https://github.com/tobiashofmann88 Google Scholar profile https://scholar.google.se/citations?user=soeWAQwAAAAJ&hl=en&oi=ao

On 4 Feb 2019, at 16:05, ClaudiaPaetzold notifications@github.com wrote:

I am trying to assemble our cleaned reads using the assemble-reads function and run into the following error:

`>(secapr_env) sysbot@ug-ubgb900-c119:/media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/trimmed$ secapr assemble_reads --input /media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/trimmed/ --output /media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/assembled/

################################################## Processing sample Zcori Traceback (most recent call last): File "/usr/local/anaconda3/envs/secapr_env/bin/secapr", line 6, in sys.exit(secapr.main.main()) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/main.py", line 50, in main args.func(args) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/assemble_reads.py", line 146, in main contig_count_df = get_stats_abyss(sample_output_folder,sample_id,sample_contig_count_dict) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/assemble_reads.py", line 251, in get_stats_abyss contig_count = count_contigs(contig_file) File "/usr/local/anaconda3/envs/secapr_env/lib/python2.7/site-packages/secapr/assemble_reads.py", line 245, in count_contigs return sum([1 for line in open(contig, 'rU').readlines() if line.startswith('>')]) IOError: [Errno 2] No such file or directory: '/media/sysbot/Daten/Niklas/SECAPR_Zanth/data/processed/assembled/Zcori.fa' ` Secpar (including abyss) was installed via conda on a Ubuntu 14.04 system. Also in the function there is no option to specify the --assembler parameter. Could there be some error in the installation? If not could you please help me identify the problem? Thank you.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/seqcap_processor/issues/13, or mute the thread https://github.com/notifications/unsubscribe-auth/AKNlRQlPGdQvr-14cM9EmE6TbHCx6oXnks5vKExHgaJpZM4ahYbs.

ClaudiaPaetzold commented 5 years ago

secapr --version prints

secapr 1.1.4

running conda update secapr tells me that all requested packages are already installed.

I have also tested Abyss separately and it runs through a representative sample without error. Also the IOError appears very fast (within seconds of starting the script). The requested outfolders (in this case "assembled/" and "assembled/stats/Zcori") are created, but there is no fasta file in there.

Thank you for your quick response and your help.

tandermann commented 5 years ago

somehow you have a very outdated version of secapr installed. just type ’conda update secapr’ to update the pipeline to its newest version.

Tobias Andermann (Hofmann) PhD student Biological and Environmental Sciences, University of Gothenburg The Antonelli Lab http://antonelli-lab.net/ | Gothenburg Global Biodiversity Centre http://ggbc.gu.se/ Carl Skottsbergs gata 22 B https://goo.gl/maps/mwGPq3HNzAN2, 413 19 Göteborg tobias.andermann@bioenv.gu.se mailto:tobias.andermann@bioenv.gu.se +46 76 090 1106 github.com/tobiashofmann88 https://github.com/tobiashofmann88 Google Scholar profile https://scholar.google.se/citations?user=soeWAQwAAAAJ&hl=en&oi=ao

On 5 Feb 2019, at 18:10, ClaudiaPaetzold notifications@github.com wrote:

secapr --version prints

secapr 1.1.4

running conda update secapr tells me that all requested packages are already installed.

I have also tested Abyss separately and it runs through a representative sample without error. Also the IOError appears very fast (within seconds of starting the script). The requested outfolders (in this case "assembled/" and "assembled/stats/Zcori") are created, but there is no fasta file in there.

Thank you for your quick response and your help.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/seqcap_processor/issues/13#issuecomment-460721256, or mute the thread https://github.com/notifications/unsubscribe-auth/AKNlRawSXCMjGkPt6AlG5QQagsMn0H3Cks5vKbsDgaJpZM4ahYbs.

ClaudiaPaetzold commented 5 years ago

I have tried to run conda update both with activated and deactivated secapr environment.

I all cases the result is

All requested packages already installed.

I have added all required channels to conda; the environments and package metadata checks come out with no error. I am working on a Ubuntu 16.04 machine and conda 4.6.3.

tandermann commented 5 years ago

That is strange. What happens if you type “conda install secapr=1.1.12”? Best, Tobi

Tobias Andermann (Hofmann) PhD student Biological and Environmental Sciences, University of Gothenburg The Antonelli Lab http://antonelli-lab.net/ | Gothenburg Global Biodiversity Centre http://ggbc.gu.se/ Carl Skottsbergs gata 22 B https://goo.gl/maps/mwGPq3HNzAN2, 413 19 Göteborg tobias.andermann@bioenv.gu.se mailto:tobias.andermann@bioenv.gu.se +46 76 090 1106 github.com/tobiashofmann88 https://github.com/tobiashofmann88 Google Scholar profile https://scholar.google.se/citations?user=soeWAQwAAAAJ&hl=en&oi=ao

On 14 Feb 2019, at 14:54, ClaudiaPaetzold notifications@github.com wrote:

I have tried to run conda update both with activated and deactivated secapr environment.

I all cases the result is

All requested packages already installed.

I have added all required channels to conda; the environments and package metadata checks come out with no error. I am working on a Ubuntu 16.04 machine and conda 4.6.3.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/seqcap_processor/issues/13#issuecomment-463634933, or mute the thread https://github.com/notifications/unsubscribe-auth/AKNlReqQAP9IgZD8Qc6q9SCNjmOUjIDnks5vNWqUgaJpZM4ahYbs.

ClaudiaPaetzold commented 5 years ago

I tried that, and shot my Anaconda installation. After I rescued it, I reupdated my conda base, then activated the env and tried the update again. Got an error:

ERROR conda.core.link:_execute(544): An error occurred while installing package 'defaults::dbus-1.10.20-0'.

So then I changed permissions for the package:

chmod +r /usr/local/anaconda3/pkgs/dbus-1.10.10-0/bin/.dbus-post-link.sh chmod +r /usr/local/anaconda3/dbus-1.10.10-0/libexec/dbus-daemon-launch-helper

Then I tried the conda install again. Now it seems to work. It's running through the first sample as I'm writing. If it runs through without error, I'm going to close this issue. Thank you for your help. Cheers

tandermann commented 5 years ago

great! otherwise if it is still causing problems you can follow the instructions at the end of the secapr installation tutorial. I added a paragraph there how to update to the development version, which gives you all the most recent upgrades. Best, Tobi

Tobias Andermann (Hofmann) PhD student Biological and Environmental Sciences, University of Gothenburg The Antonelli Lab http://antonelli-lab.net/ | Gothenburg Global Biodiversity Centre http://ggbc.gu.se/ Carl Skottsbergs gata 22 B https://goo.gl/maps/mwGPq3HNzAN2, 413 19 Göteborg tobias.andermann@bioenv.gu.se mailto:tobias.andermann@bioenv.gu.se +46 76 090 1106 github.com/tobiashofmann88 https://github.com/tobiashofmann88 Google Scholar profile https://scholar.google.se/citations?user=soeWAQwAAAAJ&hl=en&oi=ao

On 26 Feb 2019, at 16:40, ClaudiaPaetzold notifications@github.com wrote:

I tried that, and shot my Anaconda installation. After I rescued it, I reupdated my conda base, then activated the env and tried the update again. Got an error:

ERROR conda.core.link:_execute(544): An error occurred while installing package 'defaults::dbus-1.10.20-0'.

So then I changes permissions for the package:

chmod +r /usr/local/anaconda3/pkgs/dbus-1.10.10-0/bin/.dbus-post-link.sh chmod +r /usr/local/anaconda3/dbus-1.10.10-0/libexec/dbus-daemon-launch-helper

Then I tried the conda install again. Now it seems to work. It's running trough the first sample as I write Thank you for your help. Cheers

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/seqcap_processor/issues/13#issuecomment-467488216, or mute the thread https://github.com/notifications/unsubscribe-auth/AKNlReJa5LIpweYJ-UxzD5CeGVH4qecrks5vRVVWgaJpZM4ahYbs.

tandermann commented 5 years ago

p.s.: i just made a new secapr release on conda with some updates, it’s called v.1.1.14 and should install and run smoother than previous versions.

Best, Tobi

Tobias Andermann (Hofmann) PhD student Biological and Environmental Sciences, University of Gothenburg The Antonelli Lab http://antonelli-lab.net/ | Gothenburg Global Biodiversity Centre http://ggbc.gu.se/ Carl Skottsbergs gata 22 B https://goo.gl/maps/mwGPq3HNzAN2, 413 19 Göteborg tobias.andermann@bioenv.gu.se mailto:tobias.andermann@bioenv.gu.se +46 76 090 1106 github.com/tobiashofmann88 https://github.com/tobiashofmann88 Google Scholar profile https://scholar.google.se/citations?user=soeWAQwAAAAJ&hl=en&oi=ao

On 26 Feb 2019, at 17:54, Tobias Hofmann tobias.hofmann@bioenv.gu.se wrote:

great! otherwise if it is still causing problems you can follow the instructions at the end of the secapr installation tutorial. I added a paragraph there how to update to the development version, which gives you all the most recent upgrades. Best, Tobi

Tobias Andermann (Hofmann) PhD student Biological and Environmental Sciences, University of Gothenburg The Antonelli Lab http://antonelli-lab.net/ | Gothenburg Global Biodiversity Centre http://ggbc.gu.se/ Carl Skottsbergs gata 22 B https://goo.gl/maps/mwGPq3HNzAN2, 413 19 Göteborg tobias.andermann@bioenv.gu.se mailto:tobias.andermann@bioenv.gu.se +46 76 090 1106 github.com/tobiashofmann88 https://github.com/tobiashofmann88 Google Scholar profile https://scholar.google.se/citations?user=soeWAQwAAAAJ&hl=en&oi=ao

On 26 Feb 2019, at 16:40, ClaudiaPaetzold <notifications@github.com mailto:notifications@github.com> wrote:

I tried that, and shot my Anaconda installation. After I rescued it, I reupdated my conda base, then activated the env and tried the update again. Got an error:

ERROR conda.core.link http://conda.core.link/:_execute(544): An error occurred while installing package 'defaults::dbus-1.10.20-0'.

So then I changes permissions for the package:

chmod +r /usr/local/anaconda3/pkgs/dbus-1.10.10-0/bin/.dbus-post-link.sh chmod +r /usr/local/anaconda3/dbus-1.10.10-0/libexec/dbus-daemon-launch-helper

Then I tried the conda install again. Now it seems to work. It's running trough the first sample as I write Thank you for your help. Cheers

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/seqcap_processor/issues/13#issuecomment-467488216, or mute the thread https://github.com/notifications/unsubscribe-auth/AKNlReJa5LIpweYJ-UxzD5CeGVH4qecrks5vRVVWgaJpZM4ahYbs.

ClaudiaPaetzold commented 5 years ago

Thanks a lot; I will update right away. And I will close the issue now, as my analysis does run smoothly now.

Best, Claudia

AntonelliLab / seqcap_processor