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mtisza1 / Cenote-Taker3

Discover and annotate the virome
MIT License
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Failed to execute ct3_DBs/mmseqs_DBs/tmp/15439912201242243644/download.sh with error 13. #18

Closed MonicaSteffi closed 2 weeks ago

MonicaSteffi commented 3 weeks ago

Dear all,

I have successfully installed the Cenote-Taker3, but I am countering error while downloading the databases. 

running HMM database update/install
--2024-11-11 10:06:40--  https://zenodo.org/records/10840546/files/hmmscan_DBs.tgz
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.184.103.159, 188.185.79.172, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 362040652 (345M) [application/octet-stream]
Saving to: ‘ct3_DBs/hmmscan_DBs/hmmscan_DBs.tgz’

hmmscan_DBs.tgz                                                        100%[==========================================================================================================================================================================>] 345.27M  5.28MB/s    in 59s

2024-11-11 10:07:39 (5.83 MB/s) - ‘ct3_DBs/hmmscan_DBs/hmmscan_DBs.tgz’ saved [362040652/362040652]

v3.1.1/
v3.1.1/DNA_rep_HMMs.h3m
v3.1.1/Virion_HMMs.h3m
v3.1.1/Useful_Annotation_HMMs.h3m
v3.1.1/RDRP_HMMs.h3m
v3.1.1/phrogs_for_ct.h3m
running mmseqs refseq taxdb database update/install
--2024-11-11 10:07:47--  https://zenodo.org/records/10840546/files/refseq_virus_prot.fasta.gz
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.185.79.172, 188.184.103.159, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 101534419 (97M) [application/octet-stream]
Saving to: ‘ct3_DBs/mmseqs_DBs/refseq_virus_prot.fasta.gz’

refseq_virus_prot.fasta.gz                                             100%[==========================================================================================================================================================================>]  96.83M  5.80MB/s    in 15s

2024-11-11 10:08:02 (6.45 MB/s) - ‘ct3_DBs/mmseqs_DBs/refseq_virus_prot.fasta.gz’ saved [101534419/101534419]

--2024-11-11 10:08:04--  https://zenodo.org/records/10840546/files/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.184.103.159, 188.185.79.172, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3669983 (3.5M) [application/octet-stream]
Saving to: ‘ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv’

ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv                 100%[==========================================================================================================================================================================>]   3.50M  4.77MB/s    in 0.7s

2024-11-11 10:08:05 (4.77 MB/s) - ‘ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv’ saved [3669983/3669983]

createdb ct3_DBs/mmseqs_DBs/refseq_virus_prot.fasta ct3_DBs/mmseqs_DBs/refseq_virus_prot_taxDB

MMseqs Version:         15.6f452
Database type           0
Shuffle input database  true
Createdb mode           0
Write lookup file       1
Offset of numeric ids   0
Compressed              0
Verbosity               3

Converting sequences
[681549] 1s 265ms
Time for merging to refseq_virus_prot_taxDB_h: 0h 0m 0s 167ms
Time for merging to refseq_virus_prot_taxDB: 0h 0m 0s 272ms
Database type: Aminoacid
Time for processing: 0h 0m 2s 810ms
Create directory ct3_DBs/mmseqs_DBs/tmp
createtaxdb ct3_DBs/mmseqs_DBs/refseq_virus_prot_taxDB ct3_DBs/mmseqs_DBs/tmp --tax-mapping-file ct3_DBs/mmseqs_DBs/refseq_virus_prot_taxids.mmseqs_fmt.tsv

MMseqs Version:         15.6f452
NCBI tax dump directory
Taxonomy mapping file   ct3_DBs/mmseqs_DBs/refseq_virus_prot_taxids.mmseqs_fmt.tsv
Taxonomy mapping mode   0
Taxonomy db mode        1
Threads                 56
Verbosity               3

Failed to execute ct3_DBs/mmseqs_DBs/tmp/createindex.sh with error 13.
running mmseqs hallmark taxdb database update/install
--2024-11-11 10:08:08--  https://zenodo.org/records/10840546/files/ct3_hallmark_nr_cd90_refseq.faa.gz
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.185.79.172, 188.184.103.159, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 53518322 (51M) [application/octet-stream]
Saving to: ‘ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.faa.gz’

ct3_hallmark_nr_cd90_refseq.faa.gz                                     100%[==========================================================================================================================================================================>]  51.04M  5.51MB/s    in 9.5s

2024-11-11 10:08:17 (5.39 MB/s) - ‘ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.faa.gz’ saved [53518322/53518322]

--2024-11-11 10:08:19--  https://zenodo.org/records/10840546/files/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.184.103.159, 188.185.79.172, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3669983 (3.5M) [application/octet-stream]
Saving to: ‘ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv.1’

ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv.1               100%[==========================================================================================================================================================================>]   3.50M  5.24MB/s    in 0.7s

2024-11-11 10:08:20 (5.24 MB/s) - ‘ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv.1’ saved [3669983/3669983]

createdb ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.faa ct3_DBs/mmseqs_DBs/ct3_hallmark.taxDB

MMseqs Version:         15.6f452
Database type           0
Shuffle input database  true
Createdb mode           0
Write lookup file       1
Offset of numeric ids   0
Compressed              0
Verbosity               3

Converting sequences
[173721] 0s 422ms
Time for merging to ct3_hallmark.taxDB_h: 0h 0m 0s 52ms
Time for merging to ct3_hallmark.taxDB: 0h 0m 0s 194ms
Database type: Aminoacid
Time for processing: 0h 0m 1s 137ms
createtaxdb ct3_DBs/mmseqs_DBs/ct3_hallmark.taxDB ct3_DBs/mmseqs_DBs/tmp --tax-mapping-file ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv

MMseqs Version:         15.6f452
NCBI tax dump directory
Taxonomy mapping file   ct3_DBs/mmseqs_DBs/ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv
Taxonomy mapping mode   0
Taxonomy db mode        1
Threads                 56
Verbosity               3

Failed to execute ct3_DBs/mmseqs_DBs/tmp/createindex.sh with error 13.
running mmseqs CDD database update/install
--2024-11-11 10:08:21--  https://zenodo.org/records/10840546/files/cddid_all.tbl
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.184.103.159, 188.185.79.172, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 34485955 (33M) [application/octet-stream]
Saving to: ‘ct3_DBs/mmseqs_DBs/cddid_all.tbl’

cddid_all.tbl                                                          100%[==========================================================================================================================================================================>]  32.89M  6.01MB/s    in 5.7s

2024-11-11 10:08:27 (5.75 MB/s) - ‘ct3_DBs/mmseqs_DBs/cddid_all.tbl’ saved [34485955/34485955]

databases CDD ct3_DBs/mmseqs_DBs/CDD ct3_DBs/mmseqs_DBs/tmp

MMseqs Version:                 15.6f452
Tsv                             false
Force restart with latest tmp   false
Remove temporary files          false
Compressed                      0
Threads                         56
Verbosity                       3

Failed to execute ct3_DBs/mmseqs_DBs/tmp/15439912201242243644/download.sh with error 13.
--2024-11-11 10:08:27--  https://zenodo.org/records/10840546/files/viral_cdds_and_pfams_191028.txt
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.185.79.172, 188.184.103.159, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15322 (15K) [text/plain]
Saving to: ‘ct3_DBs/viral_cdds_and_pfams_191028.txt’

viral_cdds_and_pfams_191028.txt                                        100%[==========================================================================================================================================================================>]  14.96K  --.-KB/s    in 0.02s

2024-11-11 10:08:27 (626 KB/s) - ‘ct3_DBs/viral_cdds_and_pfams_191028.txt’ saved [15322/15322]

what could be the reason for this?

mtisza1 commented 2 weeks ago

Hi Monica,

Thanks for opening this issue. "error 13" in bash means that you don't have permission to execute the file.

Can you check your permissions for the failed .sh files specifically and the subdirectory you're working in more generally, using ls -l or something similar.

I hope this points you in the right direction.

Mike