search

lpantano / seqcluster

small RNA analysis from NGS data
http://seqcluster.readthedocs.io
MIT License
35 stars 17 forks source link

issue in seqcluster prepare #39

Closed kisun closed 5 years ago

kisun commented 5 years ago

HI, The command for running "prepare" step was:

seqcluster prepare -c files-collapsed -o ${outdir}/prepd-seqs --minl 17 --minc 2 --maxl 45 The error message I got is:

Traceback (most recent call last): File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/bin/seqcluster", line 11, in <module> load_entry_point('seqcluster==1.2.4a14', 'console_scripts', 'seqcluster')() File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/lib/python3.6/site-packages/seqcluster/command_line.py", line 25, in main prepare(kwargs["args"]) File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/lib/python3.6/site-packages/seqcluster/prepare_data.py", line 38, in prepare seq_l, sample_l = _read_fastq_files(f, args) File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/lib/python3.6/site-packages/seqcluster/prepare_data.py", line 103, in _read_fastq_files with open_fastq(cols[0]) as handle: AttributeError: __enter__ Can you please tell me what could I do to solve this issue?

Thanks!

lpantano commented 5 years ago

Hi, sorry for this error.

Can you show me what you have in the file files-collapsed?

Maybe the format is not the expected one.

cheers

Lorena Pantano, P.h.D

Research Scientist

Biostatistics Department

Harvard T.H. Chan School of Public Health

https://mirtop.github.io

https://lpantano.github.io

I'll be out of office from Dec-17th to Jan9th

On Mon, Jan 21, 2019 at 4:49 AM Kisun Pokharel notifications@github.com wrote:

HI, The command for running "prepare" step was:

seqcluster prepare -c files-collapsed -o ${outdir}/prepd-seqs --minl 17 --minc 2 --maxl 45 The error message I got is:

Traceback (most recent call last): File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/bin/seqcluster", line 11, in load_entry_point('seqcluster==1.2.4a14', 'console_scripts', 'seqcluster')() File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/lib/python3.6/site-packages/seqcluster/command_line.py", line 25, in main prepare(kwargs["args"]) File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/lib/python3.6/site-packages/seqcluster/prepare_data.py", line 38, in prepare seq_l, sample_l = _read_fastq_files(f, args) File "/wrk/kipokh/DONOTREMOVE/bioconda3_env/bioconda_tools/lib/python3.6/site-packages/seqcluster/prepare_data.py", line 103, in _read_fastq_files with open_fastq(cols[0]) as handle: AttributeError: enter Can you please tell me what could I do to solve this issue?

Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/lpantano/seqcluster/issues/39, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HIVz2za07DvFqdowlDI2jo2kb9oPks5vFY1BgaJpZM4aKdJ1 .

kisun commented 5 years ago

Hi, thanks for the quick reply. The content (6 out of 39 lines) of the files-collapsed looks like below: C1033_trimmed_trimmed.fastq C1033 C107A1_trimmed_trimmed.fastq C107A1 E1033_trimmed_trimmed.fastq E1033 E107A1_trimmed_trimmed.fastq E107A1 E251_trimmed_trimmed.fastq E251

Best wishes, Kisun

lpantano commented 5 years ago

Can you tell me whether the file is separated with tabular or space between the two columns?

kisun commented 5 years ago

It is tab-delimited file. If log file gives you some hint

INFO-seqcluster.libs.logger(24): Run prepare INFO-prepare(37): Reading sequeces INFO-prepare(136): C1033: Total read 265529 ; Total added 41038 INFO-prepare(136): C107A1: Total read 400946 ; Total added 45900

and I also see the stats.csv..but seqs.fastq and seqs.ma are empty.

lpantano commented 5 years ago

Thanks,

Do you see the INFO line for all the samples or it stops at in the middle of the processing? is it the last sample showed in the console the one in the config file?

kisun commented 5 years ago

I can see INFO line for all the samples.

lpantano commented 5 years ago

Can you check if there is a empty line at the end?

kisun commented 5 years ago

For your reference i attached you the output files. prepd-seqs.zip

kisun commented 5 years ago

Can you tell me whether the file is separated with tabular or space between the two columns?

Hi, does the sample ID need to be three-letter-code like for mirdeep2?

kisun commented 5 years ago

Can you tell me whether the file is separated with tabular or space between the two columns?

Hi, does the sample ID need to be three-letter-code like for mirdeep2?

It's now running smoothly by using new 3-letter-codes. Sorry for not trying this earlier. And thanks a lot for your effort. Best wishes, Kisun

lpantano commented 5 years ago

oh!

Thank you for figuring it out! Good luck, let me know if you find other issues.

Cheers

Lorena Pantano, P.h.D

Research Scientist

Biostatistics Department

Harvard T.H. Chan School of Public Health

https://mirtop.github.io

https://lpantano.github.io

I'll be out of office from Dec-17th to Jan9th

On Tue, Jan 22, 2019 at 6:12 PM Kisun Pokharel notifications@github.com wrote:

Can you tell me whether the file is separated with tabular or space between the two columns?

Hi, does the sample ID need to be three-letter-code like for mirdeep2?

It's now running smoothly by using new 3-letter-codes. Sorry for not trying this earlier. And thanks a lot for your effort. Best wishes, Kisun

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lpantano/seqcluster/issues/39#issuecomment-456599924, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HMlvC-NDgDLrjXdW5NKB34Ej4YnHks5vF5rygaJpZM4aKdJ1 .