zdf1987
commented
9 months ago I am glad to receive your message. I am not at a computer now, and I can't check the code immediately. But i think you can make this attempts: Delete line 4 and then run it again. This line is useless other than prevent to give a confusing warning that will appear even though it run successful. In addition, your AA file is not correct for this script. The script need several AA files to run, each of them should include homolog gene sequences (gene clusters), i.e. they are variation of a single gene. Your file seems that several different genes we're gathered. If you want do this, You should put each gene sequence in a file, respectively. Netherlessly, such a way to detect homologous is not preferred by HMMER, But by blast. An early version3.0 of easyCGTree uses blast to detect homologous, which can be found also on GitHub(earl version section of EasyCGTree 4.0). You can try it. Best regards,
张道锋 博士 河海大学 海洋学院 海洋生物研究所 地址：江苏省南京市西康路1号 邮编：210098 @. & @. 手机：15221393487
Dao-Feng Zhang, Ph. D. Institute of Marine Biology, College of Oceanography, Hohai University No.1 Xikang Road, Nanjing 210098, P.R. China. E-mail: @hhu.edu.cn & @.*** Tel：+86 15221393487
---- Replied Message ---- | From | @.> | | Date | 11/13/2023 18:51 | | To | @.> | | Cc | @.***> | | Subject | [zdf1987/EasyCGTree4] BuildHMM.pl (Issue #2) |
Hi, thanks for creating this tool/script! I downloaded and unzipped "EasyCGTree4.1-Linux.zip", and all looks good - see * below
However, my attempt to run BuildHMM.pl on my AA files** failed:
perl BuildHMM.pl -gc 00.markers_unalinged_49x Unknown warnings category 'experimental::smartmatch' at BuildHMM.pl line 4. BEGIN failed--compilation aborted at BuildHMM.pl line 4.
I run this perl version: perl -v This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi (with 44 registered patches, see perl -V for more detail)
Thanks for your help, Chris
_* Archive: EasyCGTree4.1-Linux.zip
creating: EasyCGTree4.1-Linux/ inflating: EasyCGTree4.1-Linux/BuildHMM.pl inflating: EasyCGTree4.1-Linux/EasyCGTree.pl inflating: EasyCGTree4.1-Linux/Gene_Prevelence.pl creating: EasyCGTree4.1-Linux/HMM/ inflating: EasyCGTree4.1-Linux/HMM/README.txt inflating: EasyCGTree4.1-Linux/README inflating: EasyCGTree4.1-Linux/README.TXT creating: EasyCGTree4.1-Linux/bin/ inflating: EasyCGTree4.1-Linux/bin/FastTreeMP inflating: EasyCGTree4.1-Linux/bin/astral-hybrid inflating: EasyCGTree4.1-Linux/bin/clustalo inflating: EasyCGTree4.1-Linux/bin/consenseM inflating: EasyCGTree4.1-Linux/bin/hmmbuild inflating: EasyCGTree4.1-Linux/bin/hmmsearch inflating: EasyCGTree4.1-Linux/bin/iqtree2 inflating: EasyCGTree4.1-Linux/bin/trimal inflating: EasyCGTree4.1-Linux/treeapp-options.txt
** AA file example: 00.markers_unalinged_49x/14_combined_orthos.fa
HAB125.fa MAQRARIKLISNDPQSLQKICNQIGKIAERTGVRIRGPIPLPSKRIVIPVRKSPCGNGTATFDHLEMKLHKRIIDMDAEEKSMRLLMRIHVPEDVHIEIAIERK Mhung_aa.fa MQKARIRLTGTDYQKVEEVCEKIKEIAERTGVNLAGPIPLPTRKLVVPIRKSPDGEGTATWDRWQMRVHKRLIDLDADERALRQLMRTQVPKDIGIEIVLES HLC3.fa MTVARIRLMSNSHKELDAICDEMRNIADRTGVRMRGPVHLPTRKLVVPTRKSPCGEGTQTWEKYEMRIHKRLIDIDAEERTMRQIIRLNVSRSIFVEIELMN Hmari_aa.fa MSQQARVRLAGTSPEDLDDICADVREIANKTGVELSGPVPLPTKTLEVPSRKSPDGEGTATWEHWEMRVHKRLIDIDADERALRQLMRIQVPNDVSIEIVLED Mkand_aa.fa MAQEVRLRLSSTDHYKLEEVCERIKKVVEETGAQMSGPIPLPTKRLLVPTRKSPDGEGKATWDKWEMRIHKRLIDIKGDERTIRRLMRIHIPEEVHVEIIMK
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hi, thanks for creating this tool/script! I downloaded and unzipped "EasyCGTree4.1-Linux.zip", and all looks good - see * below
However, my attempt to run BuildHMM.pl on my AA files** failed:
perl BuildHMM.pl -gc 00.markers_unalinged_49xUnknown warnings category 'experimental::smartmatch' at BuildHMM.pl line 4. BEGIN failed--compilation aborted at BuildHMM.pl line 4.I run this perl version:
perl -vThis is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi (with 44 registered patches, see perl -V for more detail)Thanks for your help, Chris
_* Archive: EasyCGTree4.1-Linux.zip
creating: EasyCGTree4.1-Linux/ inflating: EasyCGTree4.1-Linux/BuildHMM.pl inflating: EasyCGTree4.1-Linux/EasyCGTree.pl inflating: EasyCGTree4.1-Linux/Gene_Prevelence.pl creating: EasyCGTree4.1-Linux/HMM/ inflating: EasyCGTree4.1-Linux/HMM/README.txt inflating: EasyCGTree4.1-Linux/README inflating: EasyCGTree4.1-Linux/README.TXT creating: EasyCGTree4.1-Linux/bin/ inflating: EasyCGTree4.1-Linux/bin/FastTreeMP inflating: EasyCGTree4.1-Linux/bin/astral-hybrid inflating: EasyCGTree4.1-Linux/bin/clustalo inflating: EasyCGTree4.1-Linux/bin/consenseM inflating: EasyCGTree4.1-Linux/bin/hmmbuild inflating: EasyCGTree4.1-Linux/bin/hmmsearch inflating: EasyCGTree4.1-Linux/bin/iqtree2 inflating: EasyCGTree4.1-Linux/bin/trimal inflating: EasyCGTree4.1-Linux/treeapp-options.txt
** AA file example: 00.markers_unalinged_49x/14_combined_orthos.fa