issue in seqcluster prepare

[kisun]

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]

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

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On Mon, Jan 21, 2019 at 4:49 AM Kisun Pokharel ***@***.***> 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 <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! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#39>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HIVz2za07DvFqdowlDI2jo2kb9oPks5vFY1BgaJpZM4aKdJ1> .

[kisun]

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]

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

[kisun]

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]

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]

I can see INFO line for all the samples.

[lpantano]

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

[kisun]

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

[kisun]

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]

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]

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

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On Tue, Jan 22, 2019 at 6:12 PM Kisun Pokharel ***@***.***> 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 <#39 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HMlvC-NDgDLrjXdW5NKB34Ej4YnHks5vF5rygaJpZM4aKdJ1> .