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j3xugit / RaptorX-3DModeling

Note that current version does not include search of very large metagenome data. For some proteins, metagenome data is important. We will update this as soon as possible.
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To execute the script with sh will get an error “[[: not found” #6

Closed ZillaRU closed 3 years ago

ZillaRU commented 3 years ago

https://github.com/j3xugit/RaptorX-3DModeling/blob/01e7a4b78a30b89e200ec49cb6860bd9a2ae919f/BuildFeatures/BuildFeatures.sh#L1 This line need to be changed as #!/bin/bash to make the script work normally. But I still confuse with other errors.

ERROR: invalid or damaged sequence database to be searched by hhblits: /data/HHDB

And the content of /data/HHDB is as follows:

(base) myname@xxxxxxxx:/data/HHDB$ ls -l -h
total 173G
-rw------- 1 528745 9100  379 5月  26  2020 UniRef30_2020_03.md5sums
-rw------- 1 528745 9100 133G 5月  26  2020 UniRef30_2020_03_a3m.ffdata
-rw------- 1 528745 9100 644M 5月  26  2020 UniRef30_2020_03_a3m.ffindex
-rw------- 1 528745 9100 5.8G 5月  26  2020 UniRef30_2020_03_cs219.ffdata
-rw------- 1 528745 9100 581M 5月  26  2020 UniRef30_2020_03_cs219.ffindex
-rw------- 1 528745 9100  33G 5月  26  2020 UniRef30_2020_03_hhm.ffdata
-rw------- 1 528745 9100  19M 5月  26  2020 UniRef30_2020_03_hhm.ffindex

Any help? Thanks!

j3xugit commented 3 years ago

Did you revise HHDB in raptorx-external.sh to the correct path? Below is the default setting for HHDB, but you will need to change it.

the location of the HHM database to be searched by HHblits for MSA generation. Needed unless you already have an MSA and do not want to generate any new MSAs.

export HHDB=/mnt/data/RaptorXCommon/HHblits/DB/uniref30_2020_02/UniRef30_2020_02

ZillaRU commented 3 years ago

Yes. I have revised raptorx-external.sh as follows. image

ZillaRU commented 3 years ago 
(base) myname@xxxxxxxx:~/RaptorX-3DModeling-master/Server$ bash RaptorXFolder.sh -m 8 /home/rzy/RaptorX-3DModeling-master/DB00012_OUT/DB00012.seq
ERROR: invalid or damaged sequence database to be searched by hhblits: /data/HHDB
ERROR: failed to run /home/rzy/RaptorX-3DModeling-master/BuildFeatures/BuildMSAs.sh -d /home/rzy/RaptorX-3DModeling-master/Server -m 8 /home/rzy/RaptorX-3DModeling-master/DB00012_OUT/DB00012.seq
ERROR: failed to run /home/rzy/RaptorX-3DModeling-master/BuildFeatures//BuildFeatures.sh -o /home/rzy/RaptorX-3DModeling-master/Server -g -1 -m 8 -r 4 /home/rzy/RaptorX-3DModeling-master/DB00012_OUT/DB00012.seq 
(base) myname@xxxxxxxx:~/RaptorX-3DModeling-master/Server$ cd /data/HHDB
(base) myname@xxxxxxxx:/data/HHDB$ ls -h -l
total 173G
-rw------- 1 528745 9100  379 5月  26  2020 UniRef30_2020_03.md5sums
-rw------- 1 528745 9100 133G 5月  26  2020 UniRef30_2020_03_a3m.ffdata
-rw------- 1 528745 9100 644M 5月  26  2020 UniRef30_2020_03_a3m.ffindex
-rw------- 1 528745 9100 5.8G 5月  26  2020 UniRef30_2020_03_cs219.ffdata
-rw------- 1 528745 9100 581M 5月  26  2020 UniRef30_2020_03_cs219.ffindex
-rw------- 1 528745 9100  33G 5月  26  2020 UniRef30_2020_03_hhm.ffdata
-rw------- 1 528745 9100  19M 5月  26  2020 UniRef30_2020_03_hhm.ffindex
ZillaRU commented 3 years ago

Wow, it works after I changed export HHDB=/data/HHDB to /data/HHDB/UniRef30_2020_03 and altered all #!/bin/sh to #!/bin/bash for .sh scripts.😸 Thanks.