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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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BUILD FAILED #204

Closed SergeyBaikal closed 2 years ago

SergeyBaikal commented 2 years ago

Hello! I did everything as described in the manual.

(base) sergey@debian:~/WGSCoveragePlotter$ git clone "https://github.com/lindenb/jvarkit.git" Cloning into 'jvarkit'... remote: Enumerating objects: 74714, done. remote: Counting objects: 100% (6740/6740), done. remote: Compressing objects: 100% (2545/2545), done. remote: Total 74714 (delta 2898), reused 6676 (delta 2838), pack-reused 67974 Receiving objects: 100% (74714/74714), 58.21 MiB | 6.16 MiB/s, done. Resolving deltas: 100% (42097/42097), done. (base) sergey@debian:~/WGSCoveragePlotter$ cd jvarkit (base) sergey@debian:~/WGSCoveragePlotter/jvarkit$ ./gradlew wgscoverageplotter

Task :wgscoverageplotter Downloading https://repo1.maven.org/maven2/com/github/samtools/htsjdk/2.24.1/htsjdk-2.24.1.jar to /home/sergey/WGSCoveragePlotter/jvarkit/lib/com/github/samtools/htsjdk/2.24.1/htsjdk-2.24.1.jar

Task :wgscoverageplotter FAILED

FAILURE: Build failed with an exception.

BUILD FAILED in 1m 26s 1 actionable task: 1 executed

lindenb commented 2 years ago

Hi, I suppose you're working behind a server proxy. Please see https://stackoverflow.com/a/22666646 to fix this.

SergeyBaikal commented 2 years ago

Yes, I specified my ports and proxies. But I get the same result.

./gradlew -Dhttp.proxyHost=100.0.0.1 -Dhttp.proxyPort=3128 -Dhttps.proxyHost=100.0.0.1 -Dhttps.proxyPort=3128 "-Dhttp.nonProxyHosts=*.nonproxyrepos.com|localhost"

lindenb commented 2 years ago

@SergeyBaikal Hum.. I'm afraid it will be hard to debug :-)

what's the output of 

wget -O - "https://repo1.maven.org/maven2/com/github/samtools/htsjdk/2.24.1/htsjdk-2.24.1.jar " | file -
lindenb commented 2 years ago

anyway, I uploaded a fresh copy of the tool in https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH

SergeyBaikal commented 2 years ago

The program started, but swears at the input files. I am doing something wrong.

java -jar dist/wgscoverageplotter.jar --dimension 1500x500 -C -1 --clip -R /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta /home/sergey/WGSCoveragePlotter/jvarkit/aln_sort.bam --percentile median > /home/sergey/WGSCoveragePlotter/jvarkit/plot.svg [SEVERE][WGSCoveragePlotter]Error opening file: /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta htsjdk.samtools.SAMException: Error opening file: /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta

There are 3 files in the data folder. Reference 575.fasta 575.fasta.fai aln_sort.bam

lindenb commented 2 years ago

575.dict is missing al_sort.bam should be indexed

lindenb commented 2 years ago

that's a strange error anyway... what is the output of the following commands:

file  /home/sergey/WGSCoveragePlotter/jvarkit/*
head  /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta
head  /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta.fai
SergeyBaikal commented 2 years ago

How to get the file 575.dict?

lindenb commented 2 years ago

samtools dict or picard CreateSequenceDictionary

but please, show me the output of the commands above please.

SergeyBaikal commented 2 years ago 
file  /home/sergey/WGSCoveragePlotter/jvarkit/*
/home/sergey/WGSCoveragePlotter/jvarkit/575.fasta:        ASCII text, with very long lines, with CRLF line terminators
/home/sergey/WGSCoveragePlotter/jvarkit/575.fasta.fai:    ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/aln_sort.bam:     gzip compressed data, extra field, original size 0
/home/sergey/WGSCoveragePlotter/jvarkit/aln_sort.bam.bai: SAMtools BAI (BAM indexing format), with 1 reference sequences
/home/sergey/WGSCoveragePlotter/jvarkit/articles:         directory
/home/sergey/WGSCoveragePlotter/jvarkit/build.gradle:     C++ source, ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/CITATION.cff:     ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/conda:            directory
/home/sergey/WGSCoveragePlotter/jvarkit/dist:             directory
/home/sergey/WGSCoveragePlotter/jvarkit/doc:              directory
/home/sergey/WGSCoveragePlotter/jvarkit/docs:             directory
/home/sergey/WGSCoveragePlotter/jvarkit/gradle:           directory
/home/sergey/WGSCoveragePlotter/jvarkit/gradlew:          a /usr/bin/env sh script, ASCII text executable
/home/sergey/WGSCoveragePlotter/jvarkit/gradlew.bat:      DOS batch file, ASCII text, with CRLF line terminators
/home/sergey/WGSCoveragePlotter/jvarkit/jfx.mk:           HTML document, ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/lib:              directory
/home/sergey/WGSCoveragePlotter/jvarkit/LICENSE.txt:      ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/Makefile:         ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/Makefile.legacy:  ASCII text, with very long lines
/home/sergey/WGSCoveragePlotter/jvarkit/maven.mk:         ASCII text, with very long lines
/home/sergey/WGSCoveragePlotter/jvarkit/My_data:          directory
/home/sergey/WGSCoveragePlotter/jvarkit/NEWS.md:          ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/plot.svg:         empty
/home/sergey/WGSCoveragePlotter/jvarkit/README.md:        ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/settings.gradle:  ASCII text
/home/sergey/WGSCoveragePlotter/jvarkit/src:              directory
/home/sergey/WGSCoveragePlotter/jvarkit/tmp:              directory

head  /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta
>MN940575.1 Dishui Lake viropahge 8, complete genome
ATGAATACTTCTATTCCCGATAAAGCAATTTTGAAAGACATGGCGGATGCCTCTTATCAAAATAATTATAGCGATACAATAGACGGGTTCAACCTTGTTCTTCAAACTGATACTTTAAAGTTTTTTCAATCTACATATCAACCTTTTTTCGTTGTTTCAGTAAGAGGCACAGCAGACTTCCAAGACTTCCAAGCATGGATTCCAAGTGCTATAAATAATATTCAAAATACAGAAAGATATAAAATTGATACTGACGAGTTGCTAAACTTCCAGCAACAGAATCCAACCAATATTTACACATATTATGCCGTAGGTCATTCACTAGCAGGAGCAATAATAGACGCATGGTTGAAAGCAGGTTATATTACAGAAGCAAGGACATATAATCCAGCAGTATCATATACAGATCTTAATAATGAAAATATAAATAATTACAGAGTTTATAGCGACGGAGACCCTTTGTATAACATTATGGGTAGATTTGTAAAAGGTAGAAAAGAAGTAAGATCATATGTCGTTCCAAATGTTAGATGGTGGAACATAAAGGATAGGATCTTGAA
head  /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta.fai
MN940575.1  26605   54  26605   26606
SergeyBaikal commented 2 years ago

head 575.dist @HD VN:1.0 SO:unsorted @SQ SN:MN940575.1 LN:26605 M5:e3cb46cbb391cd7da2274f48249023af UR:file:///home/sergey/samtools-1.9/My_data/575.fasta

lindenb commented 2 years ago

looks fine , although the fasta is a one line long, but it shouldn't be a problem (?)

isn't there any error message after

[SEVERE][WGSCoveragePlotter]Error opening file: /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta htsjdk.samtools.SAMException: Error opening file: /home/sergey/WGSCoveragePlotter/jvarkit/575.fasta

?

SergeyBaikal commented 2 years ago

Full output: java -jar dist/wgscoverageplotter.jar --dimension 1500x500 -C -1 --clip -R /home/sergey/WGSCoveragePlotter/jvarkit/My_data/575.fasta /home/sergey/WGSCoveragePlotter/jvarkit/My_data/aln_sort.bam --percentile median > /home/sergey/WGSCoveragePlotter/jvarkit/My_data/plot.svg [SEVERE][WGSCoveragePlotter]Could not find dictionary next to reference file file:///home/sergey/WGSCoveragePlotter/jvarkit/My_data/575.fasta htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///home/sergey/WGSCoveragePlotter/jvarkit/My_data/575.fasta at htsjdk.variant.utils.SAMSequenceDictionaryExtractor$TYPE$1.extractDictionary(SAMSequenceDictionaryExtractor.java:58) at htsjdk.variant.utils.SAMSequenceDictionaryExtractor.extractDictionary(SAMSequenceDictionaryExtractor.java:170) at com.github.lindenb.jvarkit.util.bio.SequenceDictionaryUtils.extractRequired(SequenceDictionaryUtils.java:184) at com.github.lindenb.jvarkit.tools.bam2graphics.WGSCoveragePlotter.doWork(WGSCoveragePlotter.java:289) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:958) at com.github.lindenb.jvarkit.tools.bam2graphics.WGSCoveragePlotter.main(WGSCoveragePlotter.java:617) [INFO][Launcher]wgscoverageplotter Exited with failure (-1)

lindenb commented 2 years ago

Could not find dictionary next to reference

yeah... the dict file was missing....

SergeyBaikal commented 2 years ago

I added the file but the output is the same. Not sure how it should look right. head 575.dist @HD VN:1.0 SO:unsorted @SQ SN:MN940575.1 LN:26605 M5:e3cb46cbb391cd7da2274f48249023af UR:file:///home/sergey/samtools-1.9/My_data/575.fasta

lindenb commented 2 years ago

the 575.dict should be in the same folder than 575.fa.

your command shows that the 575.fa was in home/sergey/samtools-1.9/My_data/ not in /home/sergey/WGSCoveragePlotter/jvarkit/My_data/

?

SergeyBaikal commented 2 years ago

Sorry. I'm stupid. Instead of dict, I wrote dist... Everything worked out! Great picture to post! Thank you!