Merge paired-end sequences in micca

[altinok68]

Hello, I am using micca, my file name is P1_1.fq and P1_2.fq. When I used "micca mergepairs -i fastq/P1_1.fastq -o merged.fastq -l 100 -d 30" command, "P1_1.fastq: unable to find pattern '_R1', SKIP" error come up. I changed the file name as P1_R1.fq and P1_R2.fq and same error occurred. Can you help me how can I solve the problem. Thanks in advance Best wishes

[davidealbanese]

@altinok68, if your file names are P1_R1.fq and P1_R2.fq you should run:

micca mergepairs -i fastq/P1_R1.fq -o merged.fastq -l 100 -d 30

note that the extension of P1_R1 is fq and not fastq.

Cheers, Davide

[altinok68]

Dear Davide, Thank you for your information best wishes, -- ilhan Altinok Karadeniz Technical University Faculty of Marine Sciences 61530 Surmene, Trabzon, TURKEY Ph: 90 462 377 8083 Fax: 90 462 752 2158 Email:ialtinok@ktu.edu.tr ialtinok@ktu.edu.tr http://aves.ktu.edu.tr/ialtinok/ http://enformatik.ktu.edu.tr/eakademik/3465/ https://www.researchgate.net/profile/Ilhan_Altinok https://orcid.org/0000-0003-3475-521X https://orcid.org/0000-0003-3475-521X http://enformatik.ktu.edu.tr/eakademik/3465/

On Wed, Apr 8, 2020 at 11:08 AM Davide Albanese notifications@github.com wrote:

@altinok68 https://github.com/altinok68, if your file names are P1_R1.fq and P1_R2.fq you should run:

micca mergepairs -i fastq/P1_R1.fq -o merged.fastq -l 100 -d 30

note that the extension of P1_R1 is fq and not fastq.

Cheers, Davide

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[altinok68]

Dear David,

I have fastq files (IK0-5_1.fastq and IK0-5_2.fastq) and run the following command

(base) ilhan@ilhan-VirtualBox:~/metagenome$ micca merge -i fastq/IK0-5_1.fastq -o merged.fastq

get the following error message;

Error: [Errno 2] No such file or directory: 'fastq/IK0-5_1.fastq'

I renamed the fastq file as IK0-5_R1.fastq and IK0-5_R2.fastq and run the following command

(base) ilhan@ilhan-VirtualBox:~/metagenome$ micca merge -i fastq/*R1.fastq -o merged.fastq

get the following error message;

Error: [Errno 2] No such file or directory: 'fastq/*R1.fastq'

I tried different command and get the same error messages

(base) ilhan@ilhan-VirtualBox:~/metagenome$ micca merge -i fastq/*.fastq -o merged.fastq

Error: [Errno 2] No such file or directory: 'fastq/*.fastq'

(base) ilhan@ilhan-VirtualBox:~/metagenome$ micca merge -i fastq/*_R1.fastq -o merged.fastq

Error: [Errno 2] No such file or directory: 'fastq/*_R1.fastq'

(base) ilhan@ilhan-VirtualBox:~/metagenome$ micca merge -i fastq/*_1.fastq -o merged.fastq

Error: [Errno 2] No such file or directory: 'fastq/*_1.fastq'

Can you help me about this problem?

Best wishes -- ilhan Altinok Karadeniz Technical University Faculty of Marine Sciences 61530 Surmene, Trabzon, TURKEY Ph: 90 462 377 8083 Fax: 90 462 752 2158 Email:ialtinok@ktu.edu.tr ialtinok@ktu.edu.tr http://aves.ktu.edu.tr/ialtinok/ http://enformatik.ktu.edu.tr/eakademik/3465/ https://www.researchgate.net/profile/Ilhan_Altinok https://orcid.org/0000-0003-3475-521X https://orcid.org/0000-0003-3475-521X http://enformatik.ktu.edu.tr/eakademik/3465/

On Wed, Apr 8, 2020 at 11:08 AM Davide Albanese notifications@github.com wrote:

@altinok68 https://github.com/altinok68, if your file names are P1_R1.fq and P1_R2.fq you should run:

micca mergepairs -i fastq/P1_R1.fq -o merged.fastq -l 100 -d 30

note that the extension of P1_R1 is fq and not fastq.

Cheers, Davide

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compmetagen/micca/issues/25#issuecomment-610815946, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMMBFHTX3OHUNCNDOBIW7GDRLQWGLANCNFSM4LXZ4O4A .

[davidealbanese]

Dear @altinok68, given two files IK0-5_1.fastq and IK0-5_2.fastq note that the direction of the sequences are defined by the strings _1 and _2 while the sample ID is IK0-5. Therefore, you would run the command:

micca mergepairs -i fastq/IK0-5_1.fastq -o merged.fastq -p "_1" -e "_2"

(default values are _R1 and _R2 for -p and -e, respectively).

See the latest note in https://micca.readthedocs.io/en/latest/pairedend_97.html#merge-paired-end-sequences and the page https://micca.readthedocs.io/en/latest/commands/mergepairs.html

[altinok68]

Dear David, Thank you for your prompt reply. I entered the script that you send me but I get the following error.

(base) ilhan@ilhan-VirtualBox:~/metagenome$ micca merge -i fastq/IK0-5_1.fastq -o merged.fastq -p "_1" -e "_2"

usage: micca merge [-h] -i FILE [FILE ...] -o FILE [-s SEP] [-f {fastq,fasta}]

micca merge: error: unrecognized arguments: -p _1 -e _2

best wishes,

ilhan

On Mon, Apr 20, 2020 at 1:05 PM Davide Albanese notifications@github.com wrote:

Dear @altinok68 https://github.com/altinok68, given two files IK0-5_1.fastq and IK0-5_2.fastq note that the direction of the sequences are defined by the strings _1 and _2 while the sample ID is IK0-5. Therefore, you would run the command:

micca merge -i fastq/IK0-5_1.fastq -o merged.fastq -p "_1" -e "_2"

(default values are _R1 and _R2 for -p and -e, respectively).

See the latest note in https://micca.readthedocs.io/en/latest/pairedend_97.html#merge-paired-end-sequences and the page https://micca.readthedocs.io/en/latest/commands/mergepairs.html

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compmetagen/micca/issues/25#issuecomment-616446126, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMMBFHWQSJ6S6XJSRM7MRJLRNQM7JANCNFSM4LXZ4O4A .

[davidealbanese]

micca mergepairs and not micca merge, I apologize for the error.

[altinok68]

Dear David, This time following error occurred.

(base) ilhan@ilhan-VirtualBox:~/metagenome$ micca mergepairs -i fastq/IK0-5_1.fastq -o merged.fastq -p _1 -e _2

IK0-5_2.fastq: file does not exist or is not a regular file, SKIP -- Prof. Dr. ilhan Altinok Karadeniz Technical University Faculty of Marine Sciences 61530 Surmene, Trabzon, TURKEY Ph: 90 462 377 8083 Fax: 90 462 752 2158 Email:ialtinok@ktu.edu.tr ialtinok@ktu.edu.tr http://aves.ktu.edu.tr/ialtinok/ http://enformatik.ktu.edu.tr/eakademik/3465/ https://www.researchgate.net/profile/Ilhan_Altinok https://orcid.org/0000-0003-3475-521X https://orcid.org/0000-0003-3475-521X http://enformatik.ktu.edu.tr/eakademik/3465/

On Mon, Apr 20, 2020 at 3:32 PM Davide Albanese notifications@github.com wrote:

micca mergepairs and not micca merge, I apologize for the error.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compmetagen/micca/issues/25#issuecomment-616522652, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMMBFHRMOQYIIGIFOGLMHP3RNQ6E7ANCNFSM4LXZ4O4A .

[davidealbanese]

Dear @altinok68,

do you have the file IK0-5_2.fastq in the directory ~/metagenome/fastq?

[altinok68]

yes I have

Original files were .fastq.gz, they were gunzipped in the termimal*

On Mon, Apr 20, 2020 at 4:02 PM Davide Albanese notifications@github.com wrote:

Dear @altinok68 https://github.com/altinok68,

do you have the file IK0-5_2.fastq in the directory ~/metagenome/fastq?

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[davidealbanese]

Please post the output of ls -l ~/metagenome/fastq, thanks

[altinok68]

(base) ilhan@ilhan-VirtualBox:~$ ls -l ~/metagenome

total 410812

drwxr-xr-x 2 ilhan ilhan 4096 Nis 19 10:04 fastq-join_joined

-rw-r--r-- 1 ilhan ilhan 37962135 Nis 18 11:53 IK0-5M_1

-rwxrwx--- 1 ilhan ilhan 68961368 Nis 16 08:54 IK0-5M_1.fastq

-rw-r--r-- 1 ilhan ilhan 37939759 Nis 18 11:54 IK0-5M_2

-rwxrwx--- 1 ilhan ilhan 68961368 Nis 16 08:53 IK0-5M_2.fastq

-rw-r--r-- 1 ilhan ilhan 0 Nis 20 16:32 merged.fastq

On Mon, Apr 20, 2020 at 4:31 PM Davide Albanese notifications@github.com wrote:

Please post the output of ls -l ~/metagenome/fastq, thanks

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[davidealbanese]

Dear @altinok68, FASTQ files are not in a fastq folder. It seems to me that you don't have the proper background to run a command line tool like micca, so I suggest you to get help from a bioinformatician.

Regards, Davide

[altinok68]

Dear David,

This is last question.

After reinstalling micca, I download garda file to play with the commands and get the following error.

(base) ilhan@ilhan-VirtualBox:~$ cd garda

(base) ilhan@ilhan-VirtualBox:~/garda$ micca mergepairs -i fastq/_R1.fastq -o merged.fastq -l 100 -d 30

Error: a bytes-like object is required, not 'str' ilhan

On Mon, Apr 20, 2020 at 5:02 PM Davide Albanese notifications@github.com wrote:

Dear @altinok68 https://github.com/altinok68, FASTQ files are not in a fastq folder. It seems to me that you don't have the proper background to run a command line tool like micca, so I suggest you to get help from a bioinformatician.

Regards, Davide

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