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HingeAssembler / HINGE

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"
http://genome.cshlp.org/content/27/5/747.full.pdf+html?sid=39918b0d-7a7d-4a12-b720-9238834902fd
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cannot open ./reads.fasta for 'r' #151

Open gabster opened 6 years ago

gabster commented 6 years ago

when trying to download the ecoli reads for the Hinge demo, I get the following message: cannot open ./reads.fasta for 'r'. How can I solve this? Thanks, Gabi

govinda-kamath commented 6 years ago

Could you run this command in the demo?

seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta

Is there a reads.fasta in the current directory?

gabster commented 6 years ago

Hi Govinda, thanks for the email. The problem was that I did not realize that the data needed to be downloaded from the website via wget. I did not know that the commands on the website were incomplete. It is solved now. Thanks Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Govinda Kamath [mailto:notifications@github.com] Gesendet: Mittwoch, 22. August 2018 17:03 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Author Betreff: Re: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

Could you run this command in the demo?

seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta

Is there a reads.fasta in the current directory?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/HingeAssembler/HINGE/issues/151#issuecomment-415064209, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YR7K4jSbEH0yw_KcXZblC8haaYBZks5uTXKwgaJpZM4WHum4.

gabster commented 6 years ago

Hi there, Every time I try to run the command below, I get the error message ‘command not found’. What can I do? Thanks

hinge filter --db ecoli --las ecoli.las -x ecoli --config ../../utils/nominal.ini hinge: command not found

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Govinda Kamath [mailto:notifications@github.com] Gesendet: Mittwoch, 22. August 2018 17:03 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Author Betreff: Re: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

Could you run this command in the demo?

seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta

Is there a reads.fasta in the current directory?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/HingeAssembler/HINGE/issues/151#issuecomment-415064209, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YR7K4jSbEH0yw_KcXZblC8haaYBZks5uTXKwgaJpZM4WHum4.

govinda-kamath commented 6 years ago

Have you run

source utils/setup.sh

That should set up the relevant paths.

gabster commented 6 years ago

Hi Govinda, Thanks very much for coming back to me. yes I had run

source utils/setup.sh.

The problem that I encounter now is:

“hinge: line 10: Reads_filter: command not found”

Thanks

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Govinda Kamath [mailto:notifications@github.com] Gesendet: Donnerstag, 23. August 2018 17:56 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Author Betreff: Re: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

Have you run

source utils/setup.sh

That should set up the relevant paths.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/HingeAssembler/HINGE/issues/151#issuecomment-415469279, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YS0QHfkyt4xruDJ_-vvJLb0_IPaTks5uTtCcgaJpZM4WHum4.

govinda-kamath commented 6 years ago

It looks like the path set up did not work. I'm not completely sure why. @fxia22 any ideas?

fxia22 commented 6 years ago

@govinda-kamath It looks like either the build failed or the path is not setup correctly. @gabster can you show us the output of ls -lAh HINGE/inst/lib/hinge? Thanks.

gabster commented 6 years ago

Hi Fei,

ls -lAh HINGE/inst/lib/hinge ls: cannot access 'HINGE/inst/lib/hinge': No such file or directory

I have installed ‘HINGE’ according to information given in GitHub Cheers G

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Fei Xia [mailto:notifications@github.com] Gesendet: Montag, 27. August 2018 02:19 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Mention Betreff: Re: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

@govinda-kamathhttps://github.com/govinda-kamath It looks like either the build failed or the path is not setup correctly. @gabsterhttps://github.com/gabster can you show us the output of ls -lAh HINGE/inst/lib/hinge? Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/HingeAssembler/HINGE/issues/151#issuecomment-416083875, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YSjM9G28Szvmsg43Eky1Dv-1njtiks5uUzr3gaJpZM4WHum4.

gabster commented 6 years ago

Hi again, this is what I get when I put ls –lah in the HINGE folder

HINGE$ ls -lah total 116K drwxrwxr-x 13 gabriele gabriele 4,0K Aug 23 18:15 . drwxr-xr-x 49 gabriele gabriele 4,0K Aug 27 12:28 .. drwxrwxr-x 2 gabriele gabriele 4,0K Aug 22 15:02 build -rw-rw-r-- 1 gabriele gabriele 186 Aug 22 14:57 CMakeLists.txt drwxrwxr-x 3 gabriele gabriele 4,0K Aug 22 17:29 data -rw-rw-r-- 1 gabriele gabriele 1,3K Aug 22 14:57 default.nix drwxrwxr-x 7 gabriele gabriele 4,0K Aug 22 14:57 demo drwxrwxr-x 5 gabriele gabriele 4,0K Aug 22 14:57 docker drwxrwxr-x 9 gabriele gabriele 4,0K Aug 22 15:00 .git -rw-rw-r-- 1 gabriele gabriele 119 Aug 22 14:57 .gitignore -rw-rw-r-- 1 gabriele gabriele 594 Aug 22 14:57 .gitmodules -rw-rw-r-- 1 gabriele gabriele 1,8K Aug 23 18:15 HINGE code demo -rw-rw-r-- 1 gabriele gabriele 2,7K Aug 22 14:57 licence.txt drwxrwxr-x 2 gabriele gabriele 4,0K Aug 22 14:57 misc drwxrwxr-x 10 gabriele gabriele 4,0K Aug 22 15:21 numpy -rw-rw-r-- 1 gabriele gabriele 4,9K Aug 22 14:57 parameter_description.md -rw-rw-r-- 1 gabriele gabriele 5,7K Aug 22 14:57 README.md -rw-rw-r-- 1 gabriele gabriele 213 Aug 22 14:57 requirements_frozen.txt -rw-rw-r-- 1 gabriele gabriele 7,7K Aug 22 14:57 requirements.nix -rw-rw-r-- 1 gabriele gabriele 36 Aug 22 14:57 requirements_override.nix drwxrwxr-x 2 gabriele gabriele 4,0K Aug 22 14:57 scripts -rw-rw-r-- 1 gabriele gabriele 148 Aug 22 14:57 shell.nix drwxrwxr-x 10 gabriele gabriele 4,0K Aug 22 14:57 src drwxrwxr-x 6 gabriele gabriele 4,0K Aug 22 14:57 thirdparty -rw-rw-r-- 1 gabriele gabriele 778 Aug 22 14:57 .travis.yml drwxrwxr-x 2 gabriele gabriele 4,0K Aug 22 14:57 utils

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Fei Xia [mailto:notifications@github.com] Gesendet: Montag, 27. August 2018 02:19 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Mention Betreff: Re: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

@govinda-kamathhttps://github.com/govinda-kamath It looks like either the build failed or the path is not setup correctly. @gabsterhttps://github.com/gabster can you show us the output of ls -lAh HINGE/inst/lib/hinge? Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/HingeAssembler/HINGE/issues/151#issuecomment-416083875, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YSjM9G28Szvmsg43Eky1Dv-1njtiks5uUzr3gaJpZM4WHum4.

gabster commented 6 years ago

Do you think there is a problem here:

./utils/build.shmake: Nothing to be done for 'all'. make: Nothing to be done for 'all'. make: Nothing to be done for 'all'. gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/usr/local/hdf5/include -L/usr/local/hdf5/lib -o dextract dextract.c DB.c QV.c -lhdf5 dextract.c:23:18: fatal error: hdf5.h: No such file or directory compilation terminated. Makefile:13: recipe for target 'dextract' failed make: [dextract] Error 1 mkdir: cannot create directory ‘build’: File exists ./utils/build.sh: line 19: cmake: command not found make: No targets specified and no makefile found. Stop. make: *** No rule to make target 'install'. Stop.

If yes, how can I solve it? Thanks, Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Fei Xia [mailto:notifications@github.com] Gesendet: Montag, 27. August 2018 02:19 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Mention Betreff: Re: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

@govinda-kamathhttps://github.com/govinda-kamath It looks like either the build failed or the path is not setup correctly. @gabsterhttps://github.com/gabster can you show us the output of ls -lAh HINGE/inst/lib/hinge? Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/HingeAssembler/HINGE/issues/151#issuecomment-416083875, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YSjM9G28Szvmsg43Eky1Dv-1njtiks5uUzr3gaJpZM4WHum4.

gabster commented 6 years ago

How could I solve it? Any ideas? Thanks Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Margos, Gabriele, Dr. (LGL) Gesendet: Montag, 27. August 2018 19:14 An: 'HingeAssembler/HINGE'; HingeAssembler/HINGE Cc: Mention Betreff: AW: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

Do you think there is a problem here:

./utils/build.shmake: Nothing to be done for 'all'. make: Nothing to be done for 'all'. make: Nothing to be done for 'all'. gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/usr/local/hdf5/include -L/usr/local/hdf5/lib -o dextract dextract.c DB.c QV.c -lhdf5 dextract.c:23:18: fatal error: hdf5.h: No such file or directory compilation terminated. Makefile:13: recipe for target 'dextract' failed make: [dextract] Error 1 mkdir: cannot create directory ‘build’: File exists ./utils/build.sh: line 19: cmake: command not found make: No targets specified and no makefile found. Stop. make: *** No rule to make target 'install'. Stop.

If yes, how can I solve it? Thanks, Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Fei Xia [mailto:notifications@github.com] Gesendet: Montag, 27. August 2018 02:19 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Mention Betreff: Re: [HingeAssembler/HINGE] cannot open ./reads.fasta for 'r' (#151)

@govinda-kamathhttps://github.com/govinda-kamath It looks like either the build failed or the path is not setup correctly. @gabsterhttps://github.com/gabster can you show us the output of ls -lAh HINGE/inst/lib/hinge? Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/HingeAssembler/HINGE/issues/151#issuecomment-416083875, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YSjM9G28Szvmsg43Eky1Dv-1njtiks5uUzr3gaJpZM4WHum4.