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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
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Annotate_bins Error #301

Open Sophia-LMC opened 4 years ago

Sophia-LMC commented 4 years ago

Hi. I used annotate_bins module to annotate reassembled bins. It went wrong. My metaWRAP version is 1.2.1. Details are as follows:

(metawrap) root@wea2f9c22-bf1b-4b67-bd81-9dbfc0a7e35c-5b48bfc5b5-wwb6m:/sysu_wxie_1/TJ15_18# metawrap annotate_bins -o test12 -t 32 -b reassembly_bin/reassembled_bins
metawrap annotate_bins -o test12 -t 32 -b reassembly_bin/reassembled_bins

########################################################################################################################
#####                                          BEGIN ANNNOTAION PIPELINE!                                          #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----                              setting up output folder and copything over bins...                             -----
------------------------------------------------------------------------------------------------------------------------

metawrap path: /root/miniconda3/envs/metawrap/bin/metawrap
Will use perl5 libraries located in /root/miniconda3/envs/metawrap/lib/perl5/site_perl/5.22.0 - hopefully they are there...
/root/miniconda3/envs/metawrap/bin/metawrap-scripts/shorten_contig_names.py reassembly_bin/reassembled_bins/bin.10.strict.fa > test12/tmp_bin.fa

------------------------------------------------------------------------------------------------------------------------
-----                                         NOW ANNOTATING bin.10.strict                                         -----
------------------------------------------------------------------------------------------------------------------------

prokka --quiet --cpus 32 --outdir test12/prokka_out/bin.10.strict --prefix bin.10.strict test12/tmp_bin.fa
[12:17:18] Prokka needs blastp 2.2 or higher. Please upgrade and try again.

************************************************************************************************************************
*****                        Something went wrong with annotating bin.10.strict. Exiting...                        *****
************************************************************************************************************************

I checked the version of blastp. It came out to be 2.10.1+.

(metawrap) root@wea2f9c22-bf1b-4b67-bd81-9dbfc0a7e35c-5b48bfc5b5-wwb6m:~# blastp -version
blastp: 2.10.1+
 Package: blast 2.10.1, build May 12 2020 12:15:11

Before putting forward this issue, i had referred to #188. But it seems that i did not get a openssl error. Cause i also got something wrong with metawrap classify_bins module as described at #287 , I have replaced bin/metawrap-modules/classify_bins.sh and bin/metawrap-scripts/prune_blast_hits.py as you suggested at #287.

Any suggestion for this issue? Thank you very much.

ursky commented 4 years ago

This appears to be a different issue than #188 - your problem may just the blast version, not the openssl libraries. Looking around it looks like you might fix this by either downgrading blast or upgrading prokka: https://github.com/tseemann/prokka/issues/449. If you have a manual installation of metawrap (the direct github installation) you should be able to manipulate the software versions until prokka works.

Sophia-LMC commented 4 years ago

Thanks for your reply. I tried to update prokka to 1.14.5 as mentioned at tseemann/prokka#449, but it still did not work with a same blast issue Prokka needs blastp 2.2 or higher. Please upgrade and try again. Cause my blast database is version 5 and need blast2.9 or higher, so i prefer not to downgrade blast. So, I installed a new metaWRAP environment. After experiencing and fixing issue #193 and a tbl2asn issue[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. , the PROKKA stage finally finished.