Error in rule init pre assembly processing metatranscriptomes #619

Magdalena-PP · 2023-03-15T12:55:45Z

Magdalena-PP
Mar 15, 2023

My name is Magda, I am working with @Sofie8 on metatranscriptomics data from soil. I got an error in rule init pre assembly processing .
rule init_pre_assembly_process.txt

Could you please help me with this?

I use Atlas version: 2.14.2 Snakemake 7.18.2.

Best regards,
Magda

SilasK · 2023-03-16T08:19:08Z

SilasK
Mar 16, 2023
Maintainer

It seems your OS doesn't allow you to make the symlink /home/magdalenapp/NASSerwMPP/metatrans_out_new/S15/sequence_quality_control/S15_QC_R1.fastq.gz' -> 'S15/assembly/reads/QC_R1.fastq.gz

There are some filesystems that may not permit symlinks, but Sofie never had such a problem.

Could it be that you took over the project from Sofie and therefore you don't have write permissions for some files/folders?

could you try to make

cd <atlas dir>
mkdir -p S15/assembly/reads/
ln -s /home/magdalenapp/NASSerwMPP/metatrans_out_new/S15/sequence_quality_control/S15_QC_R1.fastq.gz S15/assembly/reads/QC_R1.fastq.gz

# and maybe 
ln -s S15/sequence_quality_control/S15_QC_R1.fastq.gz S15/assembly/reads/QC_R1.fastq.gz

0 replies

SilasK · 2023-03-16T08:22:13Z

SilasK
Mar 16, 2023
Maintainer

@Magdalena-PP You also want to try to assemble metatranscriptome only?

In this case I suggest you to install atlas from Github (see the docs) and use the branch transcriptome .

#615

1 reply

SilasK Mar 28, 2023
Maintainer

Have you seen this?

Magdalena-PP · 2023-03-16T21:51:33Z

Magdalena-PP
Mar 16, 2023
Author

Hi 😊 Sofie is analyzing my samples on her computer, and at the same time, I am trying to do it on my computer. I’ve tried the commands you proposed, and it didn’t work ☹ (snakemake) ***@***.***:~$ ln -s S15/sequence_quality_control/S15_QC_R1.fastq.gz S15/assembly/reads/QC_R1.fastq.gz ln: failed to create symbolic link 'S15/assembly/reads/QC_R1.fastq.gz': No such file or directory Do you maybe know if I can get permission for symlink on my OS? Greetings, Magda

…

-- Dr Magdalena Pacwa-Płociniczak Assistant Professor University of Silesia in Katowice Faculty of Natural Sciences | Institute of Biology, Biotechnology and Environmental Protection Jagiellonska 28, 40-032 Katowice POLAND tel. +48322009442 | mob. +48607335458 e-mail: ***@***.***> ***@***.*** <http://www.us.edu.pl/> www.us.edu.pl Please consider the environment before printing this email From: Silas Kieser ***@***.***> Sent: Thursday, March 16, 2023 9:19 AM To: metagenome-atlas/atlas ***@***.***> Cc: Magdalena-PP ***@***.***>; Author ***@***.***> Subject: Re: [metagenome-atlas/atlas] Error in rule init pre assembly processing metatranscriptomes (Discussion #619) It seems your OS doesn't allow you to make the symlink /home/magdalenapp/NASSerwMPP/metatrans_out_new/S15/sequence_quality_control/S15_QC_R1.fastq.gz' -> 'S15/assembly/reads/QC_R1.fastq.gz There are some filesystems that may not permit symlinks, but Sofie never had such a problem. Could it be that you took over the project from Sofie and therefore you don't have write permissions for some files/folders? could you try to make cd <atlas dir> mkdir -p S15/assembly/reads/ ln -s /home/magdalenapp/NASSerwMPP/metatrans_out_new/S15/sequence_quality_control/S15_QC_R1.fastq.gz S15/assembly/reads/QC_R1.fastq.gz # and maybe ln -s S15/sequence_quality_control/S15_QC_R1.fastq.gz S15/assembly/reads/QC_R1.fastq.gz — Reply to this email directly, view it on GitHub <#619 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6QG7EWEJCRRD7RRV3ZA3G3W4LEINANCNFSM6AAAAAAV3YZRW4> . You are receiving this because you authored the thread. <https://github.com/notifications/beacon/A6QG7EQTLBVXEFZC23PHL4TW4LEINA5CNFSM6AAAAAAV3YZRW6WGG33NNVSW45C7OR4XAZNRIRUXGY3VONZWS33OINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQAKFLTG.gif> Message ID: < ***@***.***> ***@***.***>

0 replies

Magdalena-PP · 2023-03-28T06:52:02Z

Magdalena-PP
Mar 28, 2023
Author

Dear Silas, Thank you for being so helpful. Now I know why my OS didn’t allow me to make the symlink – the directory with the results was a shared folder. BR, Magda

…

-- Dr Magdalena Pacwa-Płociniczak Assistant Professor University of Silesia in Katowice Faculty of Natural Sciences | Institute of Biology, Biotechnology and Environmental Protection Jagiellonska 28, 40-032 Katowice POLAND tel. +48322009442 | mob. +48607335458 e-mail: ***@***.***> ***@***.*** <http://www.us.edu.pl/> www.us.edu.pl Please consider the environment before printing this email From: Silas Kieser ***@***.***> Sent: Thursday, March 16, 2023 9:19 AM To: metagenome-atlas/atlas ***@***.***> Cc: Magdalena-PP ***@***.***>; Author ***@***.***> Subject: Re: [metagenome-atlas/atlas] Error in rule init pre assembly processing metatranscriptomes (Discussion #619) It seems your OS doesn't allow you to make the symlink /home/magdalenapp/NASSerwMPP/metatrans_out_new/S15/sequence_quality_control/S15_QC_R1.fastq.gz' -> 'S15/assembly/reads/QC_R1.fastq.gz There are some filesystems that may not permit symlinks, but Sofie never had such a problem. Could it be that you took over the project from Sofie and therefore you don't have write permissions for some files/folders? could you try to make cd <atlas dir> mkdir -p S15/assembly/reads/ ln -s /home/magdalenapp/NASSerwMPP/metatrans_out_new/S15/sequence_quality_control/S15_QC_R1.fastq.gz S15/assembly/reads/QC_R1.fastq.gz # and maybe ln -s S15/sequence_quality_control/S15_QC_R1.fastq.gz S15/assembly/reads/QC_R1.fastq.gz — Reply to this email directly, view it on GitHub <#619 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6QG7EWEJCRRD7RRV3ZA3G3W4LEINANCNFSM6AAAAAAV3YZRW4> . You are receiving this because you authored the thread. <https://github.com/notifications/beacon/A6QG7EQTLBVXEFZC23PHL4TW4LEINA5CNFSM6AAAAAAV3YZRW6WGG33NNVSW45C7OR4XAZNRIRUXGY3VONZWS33OINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQAKFLTG.gif> Message ID: < ***@***.***> ***@***.***>

1 reply

SilasK Mar 28, 2023
Maintainer

Thank you for writing back.

SilasK · 2023-03-28T06:57:50Z

SilasK
Mar 28, 2023
Maintainer

Feel free to ask again if you encounter problems.

0 replies

Magdalena-PP · 2023-03-29T19:51:05Z

Magdalena-PP
Mar 29, 2023
Author

Dear Silas, Finally, I was able to finish my metatranscriptomic analysis, but the results I obtained were weird. I am sending it as an attachment. Do you maybe know the reason? Best regards, Magda

…

-- Dr Magdalena Pacwa-Płociniczak Assistant Professor University of Silesia in Katowice Faculty of Natural Sciences | Institute of Biology, Biotechnology and Environmental Protection Jagiellonska 28, 40-032 Katowice POLAND tel. +48322009442 | mob. +48607335458 e-mail: ***@***.***> ***@***.*** <http://www.us.edu.pl/> www.us.edu.pl Please consider the environment before printing this email From: Silas Kieser ***@***.***> Sent: Tuesday, March 28, 2023 8:58 AM To: metagenome-atlas/atlas ***@***.***> Cc: Magdalena-PP ***@***.***>; Mention ***@***.***> Subject: Re: [metagenome-atlas/atlas] Error in rule init pre assembly processing metatranscriptomes (Discussion #619) Feel free to ask again if you encounter problems. — Reply to this email directly, <#619 (comment)> view it on GitHub, or <https://github.com/notifications/unsubscribe-auth/A6QG7EWN62VBNKWSLZLPB6DW6KDXTANCNFSM6AAAAAAV3YZRW4> unsubscribe. You are receiving this because you were mentioned. <https://github.com/notifications/beacon/A6QG7EV4KK56R4JPNTSBVL3W6KDXTA5CNFSM6AAAAAAV3YZRW6WGG33NNVSW45C7OR4XAZNRIRUXGY3VONZWS33OINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQAKMTGM.gif> Message ID: < ***@***.***> ***@***.***>

6 replies

Magdalena-PP Mar 30, 2023
Author

I am sending zip folder with genecatalog results and logs folder.
Magda.zip

Magdalena-PP Apr 4, 2023
Author

Hi @SilasK , did you maybe find the reason for my problem with the results from genecatalog?

SilasK Apr 5, 2023
Maintainer

I have looked at your results. I don't know what you think is weird? Do you mean the parquet files?

You can open them easily with

import pandas as pd
counts_file= "Genecatalog/counts/Nmapped_reads.parquet"

counts = pd.read_parquet(counts_file).set_index("GeneNr")

In r you have the arrow::read_parquet function

SilasK Apr 5, 2023
Maintainer

From the Nmapped reads I calculated that you have this numbers of reads mapped:

S13 13031963
S14 11319618
S15 25824461
S16 10379891
S17 10440977
S18 10379891
S46 21432934
S47 24582128
S48 22212425
S49 12260911
S50 12405066
S51 18037556
S52 19974472
S53 13367263
S54 10709324

Could you check if this corresponds to the stats/readcounts.tsv?

SilasK Apr 5, 2023
Maintainer

For your information, in the latest version of atlas I swicht to a hdf format for the coutns in the genecatalog, in order to better store genegatalogs for very large datasets. But for you the current is fine.

SilasK · 2023-04-05T11:40:35Z

SilasK
Apr 5, 2023
Maintainer

Did you do an annotation, e.g. eggNOG?

0 replies

Magdalena-PP · 2023-04-05T19:59:47Z

Magdalena-PP
Apr 5, 2023
Author

Yes, you are right; It was my mistake – because I am just learning bioinformatics – I’ve tried to open parquet files with excel… Now everything is OK. Thanks for your help 😊.

…

-- Dr Magdalena Pacwa-Płociniczak Assistant Professor University of Silesia in Katowice Faculty of Natural Sciences | Institute of Biology, Biotechnology and Environmental Protection Jagiellonska 28, 40-032 Katowice POLAND tel. +48322009442 | mob. +48607335458 e-mail: ***@***.***> ***@***.*** <http://www.us.edu.pl/> www.us.edu.pl Please consider the environment before printing this email From: Silas Kieser ***@***.***> Sent: Wednesday, April 5, 2023 1:42 PM To: metagenome-atlas/atlas ***@***.***> Cc: Magdalena-PP ***@***.***>; Mention ***@***.***> Subject: Re: [metagenome-atlas/atlas] Error in rule init pre assembly processing metatranscriptomes (Discussion #619) For your information, in the latest version of atlas I swicht to a hdf format for the coutns in the genecatalog, in order to better store genegatalogs for very large datasets. But for you the current is fine. — Reply to this email directly, view it on GitHub <#619 (reply in thread)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6QG7EQ6TA4TXCUNQPKHY7DW7VLANANCNFSM6AAAAAAV3YZRW4> . You are receiving this because you were mentioned. <https://github.com/notifications/beacon/A6QG7ET33CWRLCOUUHBORC3W7VLANA5CNFSM6AAAAAAV3YZRW6WGG33NNVSW45C7OR4XAZNRIRUXGY3VONZWS33OINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQAKRS6O.gif> Message ID: < ***@***.***> ***@***.***>

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Error in rule init pre assembly processing metatranscriptomes #619

Magdalena-PP Mar 15, 2023

Replies: 8 comments · 8 replies

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