phage_tax_classification process issue #144
Comments
|
hey, this error was described in issue #142 sorry for the inconvenience |
|
Hey, Thanks, I downloaded the database and use the --databases flag (on your doc, you describe it as --database, the "s" is missing). |
|
Hi! Nico _[7c/a72104] NOTE: Process I got the same for seeker and pprmeta (example of what I have) [a4/65f607] process > identify_fasta_MSF:metaphin... [100%] 1 of 1 ✔ |
|
hi, some tools sometimes cause errors (could be due to the input data) we set these to ignore so the pipeline continues. |
|
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.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#144 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABY5D6BX6ROWMYXQREW7FQDUEDLCBANCNFSM5D6P5Q7A>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
|
|
yep could be (e.g. ram). you could try to set the |
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_DBterminated 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.shHave you ever seen this one?
Thanks for your help!
Nico
The text was updated successfully, but these errors were encountered: