Unknown error in raw_reads_filter_v0.5.pl #43
Comments
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I am getting error with raw_reads_filter_v05.pl Please give your suggestions to rectify this error |
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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. Then send me the PS.
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Dear Dr. Meng,
Thanks for your reply. I tried Docker container but i am getting this error
code:
**************************************
(base) sridhar@sridhar-HP-Z4-G4-Workstation:~/mito$ sudo docker run -v
/home/sridhar/mito:/project --rm -it guangliangmeng/mitoz:2.3
Unable to find image 'guangliangmeng/mitoz:2.3' locally
docker: Error response from daemon: pull access denied for
guangliangmeng/mitoz, repository does not exist or may require 'docker
login'.
See 'docker run --help'.
(base) sridhar@sridhar-HP-Z4-G4-Workstation:~/mito$
*************************************
I have problem in shell the docker in to the working directory
…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.
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--
***************************************************
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>*
***************************************************
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Hi Dr. Srimku, There was a typo in your command. The correct one is guanliangmeng/mitoz:2.3 Not guangliangmeng/mitoz:2.3 |
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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
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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>*
***************************************************
|
|
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>*
***************************************************
|
|
again i am getting this error
Command used:
(base) sridhar@sridhar-HP-Z4-G4-Workstation:~/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>*
***************************************************
|
|
Hi
Sorry for my late reply, for the Chinese New Year is coming and I am out of Internet connection.
It may be a bug in the Perl script. But if your data is clean data then you can just use the 'all2' command, which will skip over the Perl script (data filtering).
PS: have you prepared a example of your input fastq files as I suggested yesterday? I would like to check what is wrong there. Thanks.
…Sent from my iPhone
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>*
***************************************************
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I am getting this error for my initial run using MitoZ. I request you to kindly help me to run MitoZ successfully.
python3 MitoZ.py all --genetic_code 1 --clade Chordata --thread_number 13 --outprefix duck-01 --fastq1 TS-COR_R1.fq.gz --fastq2 TS-COR_R2.fq.gz --fastq_read_length 300 --insert_size 300 --run_mode 2 --filter_taxa_method 1 --requiring_taxa 'Chordata'
MitoZ.py:1942: DeprecationWarning: time.clock has been deprecated in Python 3.3 and will be removed from Python 3.8: use time.perf_counter or time.process_time instead
program_begin_clock = time.clock()
2020-01-21 16:59:57
perl /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl -1 /home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R1.fq.gz -2 /home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R2.fq.gz -3 /home/sridhar/mito/release_MitoZ_v2.3/tmp/duck-01.cleandata/clean.1.fq.gz -4 /home/sridhar/mito/release_MitoZ_v2.3/tmp/duck-01.cleandata/clean.2.fq.gz -m 3 -l 15 -n 10 -q 55,20 -z
input files:
/home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R1.fq.gz
/home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R2.fq.gz
output files:
/home/sridhar/mito/release_MitoZ_v2.3/tmp/duck-01.cleandata/clean.1.fq.gz
/home/sridhar/mito/release_MitoZ_v2.3/tmp/duck-01.cleandata/clean.2.fq.gz
filter parameters:
k, keep only bases between BEG and END for each read: full length read
n, the maximun N allowed in single end reads: 10
q, the maixmum percentage of low quality (ASCII code's integer) bases allowed in single end reads: 55,20
d, Filtering duplications: False
Use of uninitialized value $r01 in chomp at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 181, line 25348.
Use of uninitialized value $r02 in chomp at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 182, line 25348.
Use of uninitialized value $r03 in chomp at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 183, line 25348.
Use of uninitialized value $r04 in chomp at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 184, line 25348.
Use of uninitialized value $r01 in exists at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 195, line 25348.
Use of uninitialized value $r02 in transliteration (tr///) at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 199, line 25348.
Use of uninitialized value $seq_len in subtraction (-) at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 261, line 25348.
Use of uninitialized value $seq_len in division (/) at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 265, line 25348.
Illegal division by zero at /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl line 265, line 25348.
Error occured when running command:
perl /home/sridhar/mito/release_MitoZ_v2.3/bin/filter/raw_reads_filter_v0.5.pl -1 /home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R1.fq.gz -2 /home/sridhar/mito/release_MitoZ_v2.3/TS-COR_R2.fq.gz -3 /home/sridhar/mito/release_MitoZ_v2.3/tmp/duck-01.cleandata/clean.1.fq.gz -4 /home/sridhar/mito/release_MitoZ_v2.3/tmp/duck-01.cleandata/clean.2.fq.gz -m 3 -l 15 -n 10 -q 55,20 -z
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