Unknown error in raw_reads_filter_v0.5.pl about mitoz HOT 8 CLOSED

On Tue, Jan 21, 2020 at 6:17 PM Guanliang MENG ***@***.***> wrote: Please give a few examples of your input fastq files. I can not determine what was going on there based on the message you posted. gzip -dc /home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R1.fq.gz | head -n 20 > test.1.fq gzip -dc /home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R2.fq.gz | head -n 20 > test.2.fq Then send me the test.1.fq and test.2.fq files. PS. 1. The mitochondrial genetic code for vertebrate is 2, not 1. 2. If you prefer to install MitoZ from source code, please run the test data first (https://github.com/linzhi2013/MitoZ/tree/master/test), to make sure everything is fine. Otherwise, please use Docker version. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#43?email_source=notifications&email_token=AOKXR54RLNX3RKFXIRHJIVLQ63VF3A5CNFSM4KJR5B4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJPTRFA#issuecomment-576665748>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOKXR55MOLV3S45GPH6R6JDQ63VF3ANCNFSM4KJR5B4A> .

On Wed, Jan 22, 2020 at 12:28 PM Guanliang MENG ***@***.***> wrote: Hi Dr. Srimku, There was a typo in your command. The correct one is guanliangmeng/mitoz:2.3 Not guangliangmeng/mitoz:2.3 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#43?email_source=notifications&email_token=AOKXR57GJC72ZURRAGFTHC3Q67VCRA5CNFSM4KJR5B4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJSOEVQ#issuecomment-577036886>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOKXR52BGDDFCBOOBXJ77L3Q67VCRANCNFSM4KJR5B4A> .

On Wed, Jan 22, 2020 at 12:40 PM Sridhar j ***@***.***> wrote: Hi Dr. Meng, sorry i did this mistake. Now i rectified it and getting this message in m.err file ************* docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/create: dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'. ************ On Wed, Jan 22, 2020 at 12:28 PM Guanliang MENG ***@***.***> wrote: > Hi Dr. Srimku, > > There was a typo in your command. > > The correct one is guanliangmeng/mitoz:2.3 > > Not guangliangmeng/mitoz:2.3 > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#43?email_source=notifications&email_token=AOKXR57GJC72ZURRAGFTHC3Q67VCRA5CNFSM4KJR5B4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJSOEVQ#issuecomment-577036886>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AOKXR52BGDDFCBOOBXJ77L3Q67VCRANCNFSM4KJR5B4A> > . > -- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: +91-452-2458212 Fax: +91-452-2459873 Mobile: +91-9751648767 Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* ***************************************************

On Wed, Jan 22, 2020 at 2:39 PM Sridhar j ***@***.***> wrote: Hi Dr, Meng, I tried with the test data. Its working fine. I have problem with my sample fastq files. I am getting this error report in m.err file gzip: /project/MR-COR_R1.fq.gz: invalid compressed data--format violated Use of uninitialized value $f04 in chomp at /project/bin/filter/ raw_reads_filter_v0.5.pl line 179, <FIN> line 16563. Use of uninitialized value $seq_len in subtraction (-) at /project/bin/filter/raw_reads_filter_v0.5.pl line 261, <RIN> line 16564. Use of uninitialized value $seq_len in division (/) at /project/bin/filter/ raw_reads_filter_v0.5.pl line 265, <RIN> line 16564. Illegal division by zero at /project/bin/filter/raw_reads_filter_v0.5.pl line 265, <RIN> line 16564. Error occured when running command: perl /project/bin/filter/raw_reads_filter_v0.5.pl -1 /project/MR-COR_R1.fq.gz -2 /project/MR-COR_R2.fq.gz -3 /project/tmp/MR-COR.cleandata/clean.1.fq.gz -4 /project/tmp/MR-COR.cleandata/clean.2.fq.gz -m 3 -l 15 -n 10 -q 55,20 -z On Wed, Jan 22, 2020 at 12:40 PM Sridhar j ***@***.***> wrote: > Hi Dr. Meng, > > sorry i did this mistake. Now i rectified it and getting this message in > m.err file > > ************* > docker: Got permission denied while trying to connect to the Docker > daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/create: > dial unix /var/run/docker.sock: connect: permission denied. > See 'docker run --help'. > ************ > > On Wed, Jan 22, 2020 at 12:28 PM Guanliang MENG ***@***.***> > wrote: > >> Hi Dr. Srimku, >> >> There was a typo in your command. >> >> The correct one is guanliangmeng/mitoz:2.3 >> >> Not guangliangmeng/mitoz:2.3 >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> <#43?email_source=notifications&email_token=AOKXR57GJC72ZURRAGFTHC3Q67VCRA5CNFSM4KJR5B4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJSOEVQ#issuecomment-577036886>, >> or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AOKXR52BGDDFCBOOBXJ77L3Q67VCRANCNFSM4KJR5B4A> >> . >> > > > -- > *************************************************** > Dr. Jayavel Sridhar > UGC-Commonwealth Doctoral Fellow-UK > Assistant Professor > Department of Biotechnology (DDE) > Madurai Kamaraj University > (University with Potential for Excellence) > Madurai-625021 > INDIA > Phone: +91-452-2458212 > Fax: +91-452-2459873 > Mobile: +91-9751648767 > Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html > <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* > *************************************************** > -- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: +91-452-2458212 Fax: +91-452-2459873 Mobile: +91-9751648767 Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* ***************************************************

On Jan 22, 2020, at 19:52, srimku ***@***.***> wrote: again i am getting this error Command used: (base) ***@***.***:~/mito/release_MitoZ_v2.3$ sudo docker run -v /home/sridhar/mito/release_MitoZ_v2.3/:/project --rm guanliangmeng/mitoz:2.3 python3 MitoZ.py all --genetic_code 5 --clade Arthropoda --insert_size 150 --thread_number 4 --fastq1 MR-COR_R1.fq.gz --fastq2 MR-COR_R2.fq.gz --outprefix MR-COR --fastq_read_length 100 1>m.log 2>m.err Report in m.err: gzip: /project/MR-COR_R1.fq.gz: invalid compressed data--format violated Use of uninitialized value $f04 in chomp at /project/bin/filter/ raw_reads_filter_v0.5.pl line 179, <FIN> line 16563. Use of uninitialized value $seq_len in subtraction (-) at /project/bin/filter/raw_reads_filter_v0.5.pl line 261, <RIN> line 16564. Use of uninitialized value $seq_len in division (/) at /project/bin/filter/ raw_reads_filter_v0.5.pl line 265, <RIN> line 16564. Illegal division by zero at /project/bin/filter/raw_reads_filter_v0.5.pl line 265, <RIN> line 16564. Error occured when running command: perl /project/bin/filter/raw_reads_filter_v0.5.pl -1 /project/MR-COR_R1.fq.gz -2 /project/MR-COR_R2.fq.gz -3 /project/tmp/MR-COR.cleandata/clean.1.fq.gz -4 /project/tmp/MR-COR.cleandata/clean.2.fq.gz -m 3 -l 15 -n 10 -q 55,20 -z On Wed, Jan 22, 2020 at 2:39 PM Sridhar j ***@***.***> wrote: > Hi Dr, Meng, > > I tried with the test data. Its working fine. I have problem with my > sample fastq files. I am getting this error report in m.err file > > gzip: /project/MR-COR_R1.fq.gz: invalid compressed data--format violated > Use of uninitialized value $f04 in chomp at /project/bin/filter/ > raw_reads_filter_v0.5.pl line 179, <FIN> line 16563. > Use of uninitialized value $seq_len in subtraction (-) at > /project/bin/filter/raw_reads_filter_v0.5.pl line 261, <RIN> line 16564. > Use of uninitialized value $seq_len in division (/) at /project/bin/filter/ > raw_reads_filter_v0.5.pl line 265, <RIN> line 16564. > Illegal division by zero at /project/bin/filter/raw_reads_filter_v0.5.pl > line 265, <RIN> line 16564. > Error occured when running command: > perl /project/bin/filter/raw_reads_filter_v0.5.pl -1 > /project/MR-COR_R1.fq.gz -2 /project/MR-COR_R2.fq.gz -3 > /project/tmp/MR-COR.cleandata/clean.1.fq.gz -4 > /project/tmp/MR-COR.cleandata/clean.2.fq.gz -m 3 -l 15 -n 10 -q 55,20 -z > > On Wed, Jan 22, 2020 at 12:40 PM Sridhar j ***@***.***> wrote: > >> Hi Dr. Meng, >> >> sorry i did this mistake. Now i rectified it and getting this message in >> m.err file >> >> ************* >> docker: Got permission denied while trying to connect to the Docker >> daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/create: >> dial unix /var/run/docker.sock: connect: permission denied. >> See 'docker run --help'. >> ************ >> >> On Wed, Jan 22, 2020 at 12:28 PM Guanliang MENG ***@***.***> >> wrote: >> >>> Hi Dr. Srimku, >>> >>> There was a typo in your command. >>> >>> The correct one is guanliangmeng/mitoz:2.3 >>> >>> Not guangliangmeng/mitoz:2.3 >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> <#43?email_source=notifications&email_token=AOKXR57GJC72ZURRAGFTHC3Q67VCRA5CNFSM4KJR5B4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJSOEVQ#issuecomment-577036886>, >>> or unsubscribe >>> <https://github.com/notifications/unsubscribe-auth/AOKXR52BGDDFCBOOBXJ77L3Q67VCRANCNFSM4KJR5B4A> >>> . >>> >> >> >> -- >> *************************************************** >> Dr. Jayavel Sridhar >> UGC-Commonwealth Doctoral Fellow-UK >> Assistant Professor >> Department of Biotechnology (DDE) >> Madurai Kamaraj University >> (University with Potential for Excellence) >> Madurai-625021 >> INDIA >> Phone: +91-452-2458212 >> Fax: +91-452-2459873 >> Mobile: +91-9751648767 >> Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html >> <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* >> *************************************************** >> > > > -- > *************************************************** > Dr. Jayavel Sridhar > UGC-Commonwealth Doctoral Fellow-UK > Assistant Professor > Department of Biotechnology (DDE) > Madurai Kamaraj University > (University with Potential for Excellence) > Madurai-625021 > INDIA > Phone: +91-452-2458212 > Fax: +91-452-2459873 > Mobile: +91-9751648767 > Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html > <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* > *************************************************** > -- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: +91-452-2458212 Fax: +91-452-2459873 Mobile: +91-9751648767 Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* *************************************************** — You are receiving this because you commented. 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