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replikation / What_the_Phage

WtP: Phage identification via nextflow and docker or singularity
https://mult1fractal.github.io/wtp-documentation/
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phage_tax_classification process issue #144

Closed ntromas closed 2 years ago

ntromas commented 2 years ago

Hi!

I am using WTP with a very large input file of contigs (10,977,373 seq)

Command used: nextflow run replikation/What_the_Phage --fasta all_contigs_Champ_2016_2020.fa --cores 12 -r v1.0.2 --workdir work --cachedir cache -profile local,docker

Error found (I repeated several time and always got this)

Error executing process > 'vogtable_database:vogtable_DB'

Caused by: Process vogtable_database:vogtable_DB terminated with an error exit status (4)

Command executed:

wget -nH http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt

Command exit status: 4

Command output: (empty)

Command error: Retrying.

--2021-09-13 14:34:46-- (try: 9) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:37:04-- (try:10) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:39:24-- (try:11) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:41:44-- (try:12) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:44:03-- (try:13) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:46:22-- (try:14) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:48:41-- (try:15) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:51:01-- (try:16) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:53:20-- (try:17) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:55:39-- (try:18) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 14:57:58-- (try:19) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Retrying.

--2021-09-13 15:00:18-- (try:20) http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt Connecting to dmk-brain.ecn.uiowa.edu (dmk-brain.ecn.uiowa.edu)|128.255.23.191|:80... failed: Connection timed out. Giving up.

Work dir: /mnt/1bcce214-6fb0-454a-99a7-df65602d98b6/What_the_Phage-master/work/f4/ceff45e1ed8c0f3222f5d9ed789304

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

Have you ever seen this one?

Thanks for your help!

Nico

mult1fractal commented 2 years ago

hey,

this error was described in issue #142 I already fixed it by directly downloading it by the OSF backup databases. This fix will hopefully come this week as it is part of a bigger WtP rework.

sorry for the inconvenience

ntromas commented 2 years ago

Hey,

Thanks, I downloaded the database and use the --databases flag (on your doc, you describe it as --database, the "s" is missing). Thanks!

ntromas commented 2 years ago

Hi! With the downloaded db, it worked, thanks! However, I got several errors. Not sure if the process for these virus pipelines worked or not. Thanks for your help,

Nico

_[7c/a72104] NOTE: Process identify_fasta_MSF:vibrant_virome_wf:vibrant_virome (1) terminated with an error exit status (1) -- Error is ignored

I got the same for seeker and pprmeta (example of what I have)

[a4/65f607] process > identify_fasta_MSF:metaphin... [100%] 1 of 1 ✔ [71/b16714] process > identify_fasta_MSF:metaphin... [100%] 1 of 1 ✔ [9b/d5db1c] process > identify_fasta_MSF:metaphin... [100%] 1 of 1 ✔ [b3/69d629] process > identify_fasta_MSF:metaphin... [ 0%] 0 of 1 [- ] process > identify_fasta_MSF:metaphin... - [- ] process > identify_fasta_MSF:metaphin... - [bd/805a47] process > identify_fasta_MSF:deepvirf... [100%] 1 of 1 ✔ [54/994a37] process > identify_fasta_MSF:deepvirf... [100%] 1 of 1 ✔ [47/be0905] process > identify_fasta_MSF:deepvirf... [100%] 1 of 1 ✔ [de/1a02f6] process > identify_fasta_MSF:virfinde... [ 0%] 0 of 1 [- ] process > identify_fasta_MSF:virfinde... - [- ] process > identify_fasta_MSF:virfinde... - [28/7fba84] process > identify_fastaMSF:pprmeta... [100%] 1 of 1, failed: 1 ✔ [- ] process > identify_fastaMSF:pprmeta... - [- ] process > identify_fastaMSF:pprmeta... - [73/bbf69e] process > identify_fastaMSF:vibrant... [100%] 1 of 1 ✔ [9d/069d17] process > identify_fastaMSF:vibrant... [100%] 1 of 1 ✔ [37/6f39e8] process > identify_fastaMSF:vibrant... [100%] 1 of 1 ✔ [7c/a72104] process > identify_fastaMSF:vibrant... [100%] 1 of 1, failed: 1 ✔ [- ] process > identify_fastaMSF:vibrant... - [- ] process > identify_fastaMSF:vibrant... - [f2/19b23e] process > identify_fasta_MSF:virnet_w... [100%] 1 of 1 ✔ [- ] process > identify_fasta_MSF:virnet_w... [ 0%] 0 of 1 [- ] process > identify_fasta_MSF:virnet_w... - [- ] process > identify_fasta_MSF:virnet_w... - [49/60e3c2] process > identify_fastaMSF:phigaro... [100%] 1 of 1 ✔ [0c/9b2399] process > identify_fastaMSF:phigaro... [100%] 1 of 1 ✔ [4d/13d3c2] process > identify_fasta_MSF:seekerw... [100%] 1 of 1, failed: 1 ✔

replikation commented 2 years ago

hi, some tools sometimes cause errors (could be due to the input data) we set these to ignore so the pipeline continues.

ntromas commented 2 years ago

Hi!

Thanks, do you think it might be due to the big size of the input or the computer capacity?

Nico

Le lun. 27 sept. 2021 16 h 57, Christian Brandt @.***> a écrit :

hi, some tools sometimes cause errors (could be due to the input data) we set these to ignore so the pipeline continues.

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replikation commented 2 years ago

yep could be (e.g. ram). you could try to set the --cores the amount of threads you have, thus spawning only one process after another (not multiples in parallel) - or remove the flag (if you are using it) will do the same