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WenchenSONG / Prophage-Hunter

Prophage Hunter Linux Version
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installation problem #2

Open mujiezhang opened 11 months ago

mujiezhang commented 11 months ago

Hi, Wenchen, prophage hunter is a nice tool for prophage detection and I have used it in web version a few years ago. However, I have several questions about it.

  1. Is the web of prophage hunter still work? I can not open it.
  2. The linux version of prophage hunter is hard to install. I have done the installation step1,2,3,4 and run prophage hunter using the provided fasta file. However, I got lots of errors like below: ''''''' Use of uninitialized value $sample in concatenation (.) or string at ../../all_script/steps/NEW_seq_aa.pl line 24, line 1418. Use of uninitialized value $sample in concatenation (.) or string at ../../all_script/steps/NEW_seq_aa.pl line 24, line 1419. Use of uninitialized value $sample in concatenation (.) or string at ../../all_script/steps/NEW_seq_aa.pl line 24, line 1420. 21/12/2023 21:47:45:545 Welcome to InterProScan-5.64-96.0 21/12/2023 21:47:45:546 Running InterProScan v5 in STANDALONE mode... on Linux 21/12/2023 21:47:50:017 RunID: node154.pi.sjtu.edu.cn_20231221_214749087_jldr 21/12/2023 21:47:57:911 Loading file /dssg/home/acct-clsjhh/clsjhh/zmj/software/prophage_hunter/Prophage-Hunter/Step1.Identifying_core_elements/HYP/seq_aa_1.fa 21/12/2023 21:47:57:914 Running the following analyses: [Pfam-36.0] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 21/12/2023 21:47:58:692 30% completed 21/12/2023 21:49:01:069 70% completed 21/12/2023 21:49:02:917 80% completed 21/12/2023 21:49:14:037 100% done: InterProScan analyses completed

Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). No fasta index found for ../Input.fa. Rebuilding, please wait.. Fasta index rebuilt. Can't open perl script "../../all_script/steps/Sequence_Extract_2.pl": No such file or directory head: cannot open 'seq.Candidate_1.Tab' for reading: No such file or directory tail: cannot open 'seq.Candidate_1.Tab' for reading: No such file or directory Can't open perl script "../../all_script/steps/Tab_to_fa.pl": No such file or directory Can't open perl script "../../all_script/steps/Tab_to_fa.pl": No such file or directory

Building a new DB, current time: 12/21/2023 21:49:17 New DB name: /dssg/home/acct-clsjhh/clsjhh/zmj/software/prophage_hunter/Prophage-Hunter/Step3.Extending_to_termini_repeats/down.Candidate_1.fa New DB title: down.Candidate_1.fa Sequence type: Nucleotide Keep MBits: T Maximum file size: 3000000000B BLAST options error: File down.Candidate_1.fa does not exist Command line argument error: Argument "query". File is not accessible: `up.Candidate_1.fa' Cannot open out.outfmt6.Candidate_1.txt: No such file or directory --- Enter matrix name --------------------------------- up to 80 characters --- --- Enter matrix author(s) ---------------------------- up to 80 characters --- --- Enter matrix copyright notice --------------------- up to 80 characters --- --- Enter matrix notes ----------------- (end with '.' on a line by itself) --- done.

Cannot open ../Step3.Extending_to_termini_repeats/Candidates_with_termini_repeats.gtf: No such file or directory Cannot open prophage.gff3: No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/PL.Candidate': No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/TO.Candidate': No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/AAC.Candidate': No such file or directory Use of uninitialized value $max_num in numeric le (<=) at ../all_script/steps/Scoring.pl line 50. cat: '../Step4.Calculating_PL_TOAAC/Candidate.seq.Tab': No such file or directory Warning: [blastp] Examining 5 or more matches is recommended Warning: [blastp] Query is Empty! 21/12/2023 21:53:09:637 Welcome to InterProScan-5.64-96.0 21/12/2023 21:53:09:638 Running InterProScan v5 in STANDALONE mode... on Linux 21/12/2023 21:53:13:724 RunID: node154.pi.sjtu.edu.cn_20231221_215313261_27e5 21/12/2023 21:53:21:784 Loading file /dssg/home/acct-clsjhh/clsjhh/zmj/software/prophage_hunter/Prophage-Hunter/Step6.Annotation/Candidate_all.seq.fa

The FASTA input file /dssg/home/acct-clsjhh/clsjhh/zmj/software/prophage_hunter/Prophage-Hunter/Step6.Annotation/Candidate_all.seq.fa is empty. Therefore there are no sequences for InterproScan to analyse Finishing... 21:53:21.880 [main] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "STEPINSTANCE" not found; SQL statement: select distinct stepinstan0.id as id1111, stepinstan0_.bottom_model as bottom_m2111, stepinstan0_.bottom_protein as bottom_p3111, stepinstan0_.step_id as step_id4111, stepinstan0_.time_created as time_cre5111, stepinstan0_.top_model as top_mode6111, stepinstan0_.top_protein as top_prot7111 from public.stepinstance stepinstan0 where stepinstan0.id not in (select stepinstan1.id from public.stepinstance stepinstan1 inner join public.stepexecution executions2 on stepinstan1.id=executions2.step_instanceid where executions2.state=?) order by stepinstan0_.id desc [42102-199] 2023-12-21 21:53:21,883 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:363] ERROR - Exception thrown by StandaloneBlackBoxMaster: javax.persistence.PersistenceException: org.hibernate.exception.SQLGrammarException: could not prepare statement at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:154) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final] at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:181) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final] at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final] at org.hibernate.query.Query.getResultList(Query.java:165) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final] at uk.ac.ebi.interpro.scan.management.dao.StepInstanceDAOImpl.retrieveUnfinishedStepInstances(StepInstanceDAOImpl.java:101) ~[interproscan-management-5.64-96.0.jar:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?] at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?] at java.lang.reflect.Method.invoke(Method.java:567) ~[?:?] at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE] ''''''

  1. do you have a plan to provide a more integative version or a easier way to install it?

Thanks!

WenchenSONG commented 10 months ago
  1. Since the web server had always been attacked, we had canceled the web service.
  2. "Can't open perl script "../../all_script/steps/Sequence_Extract_2.pl": No such file or directory" Put folder "steps" under "all_script". Please check the folder "steps" and the right path of these files from download "steps".

image

  1. Please pay attention to BGI-research.

Thanks!

mingxuLi-00 commented 4 months ago

I've encountered a similar problem, unable to find the files like '../../all_script/steps/Sequence_Extract_2.pl'. But I have already placed the 'steps' files in the correct location, they are indeed under this path. image But I also encountered this kind of error.

Looking forward to your reply. Thank you for your help！

Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). Can't open perl script "../../all_script/steps/Sequence_Extract_2.pl": No such file or directory head: cannot open 'seq.Candidate_1.Tab' for reading: No such file or directory tail: cannot open 'seq.Candidate_1.Tab' for reading: No such file or directory Can't open perl script "../../all_script/steps/Tab_to_fa.pl": No such file or directory Can't open perl script "../../all_script/steps/Tab_to_fa.pl": No such file or directory

Building a new DB, current time: 07/15/2024 16:36:49 New DB name: /home/limingxu/tools/Prophage-Hunter-main/Step3.Extending_to_termini_repeats/down.Candidate_1.fa New DB title: down.Candidate_1.fa Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B BLAST options error: File down.Candidate_1.fa does not exist Command line argument error: Argument "query". File is not accessible: `up.Candidate_1.fa' Cannot open out.outfmt6.Candidate_1.txt: No such file or directory GeneMark.hmm 400-day license. License key "/home/limingxu/.gm_key" not found. This file is neccessary in order to use GeneMark.hmm. GeneMarkS: error on last system call, error code 256 Abort program!!! Cannot open Input.fa.faa: No such file or directory Cannot open host.seq.fa: No such file or directory cut: host.seq.Tab: No such file or directory Use of uninitialized value $tmp in scalar chop at ../all_script/steps/aa_to_stats.pl line 30, line 1. Use of uninitialized value $tmp in concatenation (.) or string at ../all_script/steps/aa_to_stats.pl line 31, line 1. grep: Input.fa.gff3: No such file or directory Illegal division by zero at ../all_script/steps/Orientation.stats.pl line 21, line 1. Cannot open ../Step3.Extending_to_termini_repeats/Candidates_with_termini_repeats.gtf: No such file or directory Cannot open prophage.gff3: No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/PL.Candidate': No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/TO.Candidate': No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/AAC.Candidate': No such file or directory Use of uninitialized value $max_num in numeric le (<=) at ../all_script/steps/Scoring.pl line 50. cat: '../Step4.Calculating_PL_TOAAC/Candidate.seq.Tab': No such file or directory Warning: [blastp] Query is Empty! 15/07/2024 16:36:50:439 Welcome to InterProScan-5.63-95.0 15/07/2024 16:36:50:440 Running InterProScan v5 in STANDALONE mode... on Linux 15/07/2024 16:36:54:581 RunID: localhost.localdomain_20240715_163654476_i8vp 15/07/2024 16:37:02:669 Loading file /home/limingxu/tools/Prophage-Hunter-main/Step6.Annotation/Candidate_all.seq.fa

The FASTA input file /home/limingxu/tools/Prophage-Hunter-main/Step6.Annotation/Candidate_all.seq.fa is empty. Therefore there are no sequences for InterproScan to analyse Finishing... sort: cannot read: output.txt: No such file or directory cut: output.sorted.txt: No such file or directory cut: output.sorted.txt: No such file or directory cut: output.sorted.txt: No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/Candidate.seq.Tab': No such file or directory Cannot open ../Step3.Extending_to_termini_repeats/Candidates_with_termini_repeats.gtf: No such file or directory ls: cannot access '../Step4.Calculating_PL_TOAAC/PL.Candidate.txt': No such file or directory Error in library(glmnet) : there is no package called ‘glmnet’ Execution halted cp: cannot stat '../Step3.Extending_to_termini_repeats/Candidates_with_termini_repeats.gtf': No such file or directory cat: '../Step4.Calculating_PL_TOAAC/Candidate.gff': No such file or directory ls: cannot access '../Step6.Annotation/Candidate_.Annotation.txt': No such file or directory Cannot open ../Step7.Identifying_closest_phage/Marker.best5.txt: No such file or directory

WenchenSONG commented 4 months ago

Something error in your file address. Please remove all files, must remove all files and re-install.

Please Note: Update the absolute path to "software.list", rather Must put folder "steps" under "all_script", Then run " sh generate.sh software.list" to generate prophage_hunter_RUN.sh.

Other note like GeneMark.hmm only had 400-day license, you should update your key. "License key "/home/limingxu/.gm_key" not found."

Install ##### Install steps

  1. download and install the above softwares and update the absolute path to software.list
  2. download database "steps" from https://drive.google.com/drive/folders/18FuMPNeXBmpeAVOOb1Vc9aQYgMTD0iRZ?usp=share_link
  3. put folder "steps" under "all_script"
  4. run sh generate.sh software.list to generate prophage_hunter_RUN.sh
mingxuLi-00 commented 4 months ago

Something error in your file address. Please remove all files, must remove all files and re-install.

Please Note: Update the absolute path to "software.list", rather Must put folder "steps" under "all_script", Then run " sh generate.sh software.list" to generate prophage_hunter_RUN.sh.

Other note like GeneMark.hmm only had 400-day license, you should update your key. "License key "/home/limingxu/.gm_key" not found."

Install ##### Install steps

  1. download and install the above softwares and update the absolute path to software.list
  2. download database "steps" from https://drive.google.com/drive/folders/18FuMPNeXBmpeAVOOb1Vc9aQYgMTD0iRZ?usp=share_link
  3. put folder "steps" under "all_script"
  4. run sh generate.sh software.list to generate prophage_hunter_RUN.sh

Thank you for your reply! I will try again according to your suggestions!