oschwengers / asap Goto Github PK

Hello -

I set up a Linux virtual machine (4 CPU, 4GB MEM, 100GB disk with CentOS 8.x) to test out your pipeline.
I was able to get the example data provided to run (example-lmonocytogenes-4). However, the ABR analysis failed for each isolate. I provide the asap log file and one example standard out file below:

asap.log
Listeria_monocytogenes_SRR2982078.std.log

Looking over other issues submitted, it appears this was problematic for another user (#18).
Any thoughts or suggestions for how to get the ABR analysis to work?

Thanks

Hi all,

I had successfully run you pipeline a few months ago on an old intel MacBook Pro. I have since upgraded to the new M1 MacBook, but I am facing errors that seem to be linked to processor compatibility. Have you all had any success on implementing ASA3P with M1 hardware?

Hello there 🙋‍♂️

The readme doesn't explain very well how to setup for development,
and it has some other issues,
I think a rewrite along with this template would improve it a lot 👇
https://github.com/elsewhencode/project-guidelines/blob/master/README.sample.md

Also a Makefile would be nice to have an straight way to execute things (like script inside of package.json files) and reduce the size of the readme 🙂

I am unable to complete the install step:
$ wget https://zenodo.org/record/3780003/files/asap.tar.gz

after about 1.5 hrs, get server error and can't re-initiate. Happened twice, so I posted.

Is there another host?

ASA3P (Docker) is running -- on 40 samples -- since July 09, and looks "stuck" at java -jar /asap/share/medusa/medusa.jar (running for more than 80 hours).

What should I check to ensure if it's okay?

Hello,
I am trying to analyze nanopore data with asap. Quality control, assembly and reference mapping finish while snp and scaffolding steps are aborted and all other steps fail (check fails). Are all the features supported with nanopore data? Any help would be appreciated. I have attached the log file if needed.
Thanks,
Scott
asap.log

I wish I could give more pinpoint detail of this is the problem, but I've yet to really find a common denominator. I'm an HPC admin so I'm not the one doing the work. My user has run a bunch of E coli genomes through the pipeline and they seem to sporadically fail. I've attached a spreadsheet he made that details the run and what stages seemed to fail, as well as the log files from each of the runs. I know that probably won't be enough to determine what's happening but I figure it's a start, please let me know what else I can do to help troubleshoot.
CMH-br-test-logs.zip

When running asap-docker.sh is there a way to set the max number of threads?

Add an option to resume a former failed analysis. Skip the reanalysis of all finished per isolate steps and only re-run failed steps.

Option: --resume

This pipeline generates nice report. I have illumine single-end and pacbio sequel data. I would like to assemble using hybrid mode. Currently, the only hybrid mode supported is nanopore-pe. Can you add that support?

Hello, I am having trouble downloading the asap.tar.gz file. I have been able to successfully download the other files on zenodo, but this larger file is not working for me. I have tried downloading it directly from zenodo just by clicking on the download button, and I have also tried the wget command in command line on my Windows 10 PC. Do you have any suggestions?

I have 300 Gb of space on my hard drive available, which should be enough to download the file (which you say is 142 Gb in the manual?). I have tried this several times over the course of the past week.

The error message I am currently getting when trying to manually click the download button on zenodo is "Failed - Server problem". It seems to be failing at random points; I have gotten as far as 40 Gb downloaded, but usually it fails much earlier than that.

An error message I was getting earlier in the week while trying the wget command in the windows command prompt terminal said something to the effect that too many requests were being made? Is this an issue on my end or on zenodo's end?

Any suggestions would be much appreciated! I am new to this and haven't had much luck when trying to Google answers.

Thanks,
Julia

Hi,

First of, I just wanna say this pipeline is off the hook! it's truly amazing you have managed to streamline such a complete analysis!

However, I tested the pipeline with my own data but unfortunately the taxonomy classifcation failed, the MLST is empty, no virulence factors were detected, and phylogeny tabs present errors.

Additionally, the Annotation and Core/Pan Genome tabs show no results even though output files have been produced (I can see the files individually in the output folder). I am using a Safari browser running in Mac OS. I have tried opening the report files in Mozilla and apparently the files for Annotation and Core/Pan Genome cannot be found :(

I checked the log files for each sub-analysis and they state the following:

Taxonomy classification -->
Error: Argument "num_threads". Illegal value, expected (>=1 and =<2): 4'
Error: (CArgException::eConstraint) Argument "num_threads". Illegal value, expected (>=1 and =<2): `4'

22:47:28.862 [main] ERROR asap-taxonomy - could not exec blastn!`

MLST -->
22:46:42.614 [main] INFO asap-mlst - exec: [/asap/share/blast/bin/blastn, -query, /data/scaffolds/Agrobacterium_rhizogenes_MAFF210265/Agrobacterium_rhizogenes_MAFF210265.fasta, -db, /asap/db/mlst/mlst, -num_threads, 1, -dust, no, -word_size, 32, -ungapped, -max_target_seqs, 100000, -perc_identity, 99, -outfmt, 6 sseqid slen length nident] 22:46:42.622 [main] INFO asap-mlst - ---------------------------------------------------------------------------------------------- 22:46:47.889 [main] INFO asap-mlst -

Virulence factors -->
23:09:34.790 [main] INFO asap-vf - exec: [/asap/share/blast/bin/blastp, -query, /data/annotations/Agrobacterium_rhizogenes_MAFF210265/Agrobacterium_rhizogenes_MAFF210265.faa, -db, /asap/db/sequences/vfdb, -num_threads, 1, -culling_limit, 2, -outfmt, 6 qseqid sseqid qcovs pident evalue bitscore stitle] 23:09:34.792 [main] INFO asap-vf - ---------------------------------------------------------------------------------------------- 23:11:18.192 [main] INFO asap-vf - ---------------------------------------------------------------------------------------------- 23:11:18.841 [main] DEBUG asap-vf - delete tmp-dir

Phylogeny -->
20:34:35.820 [main] ERROR asap-phylogeny - could not exec fasttreeMP!

Would you please help me solve these issues?

Thank you very much in advance. And again, killer pipeline!

Cheers,
Pablo

Hi Oliver,
a bit silly question, how to avoid sudo privileges while using the docker container? I am on contos 7 and do not have sudo rights.
thanks,

I am working in bacterial strains isolated from insect-guts and we have several strains sequenced. Asap looks like the kind of program that will very much fit the needs of the analysis that we are looking for.

I am working on a Mac with 128GB of RAM with Mac OS X 10.13.6.

Installation of asap was smooth without any issues. So in order to see that everything is working properly, I run the tutorial/example with the ecoli data.

At the end of the run, the assembly step has failed together with the mlst analysis. I am attaching the asap.log and also the assembly log. Any suggestions?

Regards
George

asap.log
std.log

Hello, I installed ASAP following the directions in the manual, but when I try to execute the launcher, I get the error below. I am running Ubuntu 20.04, and I tried both OpenJDK v.8 and v.14. Do you know what this is about?

ps. The same happens if I try to start the docker container manually.

ASA³P:   /home/mtruglio/asap
DATA:    /home/work/pseudomonas_aeruginosa/asap
Scratch: /mnt/DataDrive/tmp
Exception in thread "main" groovy.lang.MissingPropertyException: No such property: fileName for class: bio.comp.jlu.asap.ASAP
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:66)
        at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:310)
        at bio.comp.jlu.asap.ASAP$_checkConfig_closure7$_closure19$_closure20.doCall(ASAP.groovy:445)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at groovy.lang.Closure.call(Closure.java:420)
        at groovy.lang.Closure.call(Closure.java:436)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2125)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2110)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2151)
        at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at bio.comp.jlu.asap.ASAP$_checkConfig_closure7$_closure19.doCall(ASAP.groovy:443)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at groovy.lang.Closure.call(Closure.java:420)
        at groovy.lang.Closure.call(Closure.java:436)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2125)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2110)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2151)
        at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at bio.comp.jlu.asap.ASAP$_checkConfig_closure7.doCall(ASAP.groovy:434)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at groovy.lang.Closure.call(Closure.java:420)
        at groovy.lang.Closure.call(Closure.java:436)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2125)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2110)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2151)
        at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at bio.comp.jlu.asap.ASAP.checkConfig(ASAP.groovy:403)
        at bio.comp.jlu.asap.ASAP$checkConfig.callCurrent(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:157)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:177)
        at bio.comp.jlu.asap.ASAP.run(ASAP.groovy:266)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1225)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:947)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:930)
        at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:428)
        at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
        at bio.comp.jlu.asap.ASAP.main(ASAP.groovy)

Hi, if can be of help for others, I made a tool to generate the Excel file from the command line:
https://github.com/quadram-institute-bioscience/start-asap/

It's easily installable via Miniconda with conda install -c bioconda start-asap.

I'm an HPC sysadmin so I'm kind of playing the go-between here between you guys and my user on this one. The user is saying that every time he runs a pipeline it crashes during the QC step. Looking at his logs he's getting a java.lang.IllegalStateException. I can't seem to find anything on my end that would be causing this, so hopefully you can see something in his log file that might indicate what's going on. Thanks.
CMH-dpheruth-asaplog.log

Hi all,

I successfully ran 1 genome through ASA3P and planned to run 3 more genomes through the pipeline. The 1 genome that had previously been run was successful. However, when the pipeline got to genomes 2 and 3, there are several steps that resulted in the warning "max waiting period (86400000 s) exceeded!". For both of these 2 failed genomes, the pipeline was able to complete the QC, Mapping, and SNP step. However, the VFDetection, Taxonomy, MLST, ABR, Annotation, and Scaffolding step all failed due to the max waiting period warning, which resulted in several other steps being skipped.

Could this be due to a memory issue or machine issue? I don't expect this, since one genome was successfully pushed through the pipeline. I am currently running on an iMac with Docker Container with an allocated 6 CPUs and 12gb memory.

I have also attached my ASAP.log file for reference.

2021-07-22 20:26:56.521 INFO [main] bio.comp.jlu.asap.ASAP : version: 1.3.0
2021-07-22 20:26:56.536 INFO [main] bio.comp.jlu.asap.ASAP : project-path: /data
2021-07-22 20:26:56.537 INFO [main] bio.comp.jlu.asap.ASAP : command line: [--project-dir, /data, --local]
2021-07-22 20:26:56.867 INFO [main] bio.comp.jlu.asap.ASAP : option: none -> normal execution
2021-07-22 20:26:56.871 INFO [main] bio.comp.jlu.asap.ASAP : execution mode: local
2021-07-22 20:26:56.873 INFO [main] bio.comp.jlu.asap.ASAP : slot size: 1
2021-07-22 20:26:57.492 INFO [Thread-4] b.c.j.asap.steps.GenomeConversions : finished genomeConversions step
2021-07-22 20:27:20.097 INFO [Thread-1] b.c.j.a.steps.ReferenceProcessings : finished referenceProcessings step
2021-07-22 20:27:27.583 INFO [Thread-3] b.c.j.asap.steps.SNPAnnotationSetup : build snpEff database: /data/snps/snpEff.config
2021-07-22 20:27:34.374 INFO [Thread-3] b.c.j.asap.steps.SNPAnnotationSetup : finished snpAnnotationSetup step
2021-07-22 20:28:34.104 INFO [Thread-2] b.c.jlu.asap.steps.MappingIndices : finished mappingIndices step
2021-07-22 20:28:34.275 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : start analysis: genome-id=1
2021-07-23 00:04:10.450 INFO [QC-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished qc step: genome.id=1
2021-07-23 02:25:41.578 INFO [Mapping-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished mapping step: genome.id=1
2021-07-23 04:33:42.487 INFO [SNPDetection-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished snps step: genome.id=1
2021-07-23 20:07:54.487 INFO [Assembly-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished assembly step: genome.id=1
2021-07-23 20:13:40.248 INFO [Scaffolding-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished scaffolding step: genome.id=1
2021-07-23 20:14:06.188 INFO [MLST-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished mlst step: genome.id=1
2021-07-23 20:14:51.117 ERROR [ABRDetection-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : abr step aborted! genome.id=1
java.lang.IllegalStateException: abnormal ABR exit code! exitCode=1
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83)
at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:238)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:250)
at bio.comp.jlu.asap.genomes.ABRDetectionStep.runStep(ABRDetectionStep.groovy:139)
at bio.comp.jlu.asap.genomes.ABRDetectionStep$runStep$2.callCurrent(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at bio.comp.jlu.asap.genomes.AnnotationStep$runStep$2.callCurrent(Unknown Source)
at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86)
2021-07-23 20:17:32.503 INFO [Taxonomy-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished taxonomy step: genome.id=1
2021-07-23 20:18:14.820 INFO [Annotation-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished annotation step: genome.id=1
2021-07-23 20:19:22.527 INFO [VFDetection-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : finished vf step: genome.id=1
2021-07-23 20:19:22.911 INFO [ASAP-RUN-THREAD-1] b.comp.jlu.asap.genomes.GenomeStep : finished pipeline step: genome.id=1
2021-07-23 20:19:23.237 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : start analysis: genome-id=2
2021-07-24 00:15:29.353 INFO [QC-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : finished qc step: genome.id=2
2021-07-24 02:06:01.974 INFO [Mapping-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : finished mapping step: genome.id=2
2021-07-24 02:23:24.435 INFO [SNPDetection-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : finished snps step: genome.id=2
2021-07-24 20:19:37.661 WARN [ABRDetection-Step-Thread-2] b.c.j.asap.genomes.ABRDetectionStep : max waiting period (86400000 s) exceeded!
2021-07-24 20:19:37.783 WARN [MLST-Step-Thread-2] bio.comp.jlu.asap.genomes.MLSTStep : max waiting period (86400000 s) exceeded!
2021-07-24 20:19:37.661 WARN [Taxonomy-Step-Thread-2] b.c.jlu.asap.genomes.TaxonomyStep : max waiting period (86400000 s) exceeded!
2021-07-24 20:19:37.781 WARN [VFDetection-Step-Thread-2] b.c.j.asap.genomes.VFDetectionStep : max waiting period (86400000 s) exceeded!
2021-07-24 20:19:37.661 WARN [Scaffolding-Step-Thread-2] b.c.j.asap.genomes.ScaffoldingStep : max waiting period (86400000 s) exceeded!
2021-07-24 20:19:37.661 WARN [Annotation-Step-Thread-2] b.c.jlu.asap.genomes.AnnotationStep : max waiting period (86400000 s) exceeded!
2021-07-24 20:19:39.074 WARN [Annotation-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : skip annotation step! check failed: genome.id=2
2021-07-24 20:19:39.075 WARN [ABRDetection-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : skip abr step! check failed: genome.id=2
2021-07-24 20:19:39.075 WARN [Taxonomy-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : skip taxonomy step! check failed: genome.id=2
2021-07-24 20:19:39.076 WARN [Scaffolding-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : skip scaffolding step! check failed: genome.id=2
2021-07-24 20:19:39.076 WARN [MLST-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : skip mlst step! check failed: genome.id=2
2021-07-24 20:19:39.074 WARN [VFDetection-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : skip vf step! check failed: genome.id=2
2021-07-24 22:53:25.615 INFO [Assembly-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : finished assembly step: genome.id=2
2021-07-24 22:53:26.165 INFO [ASAP-RUN-THREAD-1] b.comp.jlu.asap.genomes.GenomeStep : finished pipeline step: genome.id=2
2021-07-24 22:53:26.494 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : start analysis: genome-id=3
2021-07-25 02:36:11.002 INFO [QC-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : finished qc step: genome.id=3
2021-07-25 04:25:00.972 INFO [Mapping-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : finished mapping step: genome.id=3
2021-07-25 04:38:49.827 INFO [SNPDetection-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : finished snps step: genome.id=3
2021-07-25 22:53:41.043 WARN [VFDetection-Step-Thread-3] b.c.j.asap.genomes.VFDetectionStep : max waiting period (86400000 s) exceeded!
2021-07-25 22:53:41.043 WARN [Taxonomy-Step-Thread-3] b.c.jlu.asap.genomes.TaxonomyStep : max waiting period (86400000 s) exceeded!
2021-07-25 22:53:41.674 WARN [MLST-Step-Thread-3] bio.comp.jlu.asap.genomes.MLSTStep : max waiting period (86400000 s) exceeded!
2021-07-25 22:53:41.043 WARN [ABRDetection-Step-Thread-3] b.c.j.asap.genomes.ABRDetectionStep : max waiting period (86400000 s) exceeded!
2021-07-25 22:53:41.043 WARN [Annotation-Step-Thread-3] b.c.jlu.asap.genomes.AnnotationStep : max waiting period (86400000 s) exceeded!
2021-07-25 22:53:41.667 WARN [Scaffolding-Step-Thread-3] b.c.j.asap.genomes.ScaffoldingStep : max waiting period (86400000 s) exceeded!
2021-07-25 22:53:42.484 WARN [ABRDetection-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : skip abr step! check failed: genome.id=3
2021-07-25 22:53:44.163 WARN [VFDetection-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : skip vf step! check failed: genome.id=3
2021-07-25 22:53:44.163 WARN [Annotation-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : skip annotation step! check failed: genome.id=3
2021-07-25 22:53:44.163 WARN [Taxonomy-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : skip taxonomy step! check failed: genome.id=3
2021-07-25 22:53:44.163 WARN [Scaffolding-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : skip scaffolding step! check failed: genome.id=3
2021-07-25 22:53:44.163 WARN [MLST-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : skip mlst step! check failed: genome.id=3
2021-07-26 03:05:28.957 INFO [Assembly-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : finished assembly step: genome.id=3
2021-07-26 03:05:29.021 INFO [ASAP-RUN-THREAD-1] b.comp.jlu.asap.genomes.GenomeStep : finished pipeline step: genome.id=3
2021-07-26 03:06:19.182 INFO [Phylogeny-Analysis-Thread] b.c.jlu.asap.analyses.AnalysisStep : finished phylogeny step
2021-07-26 03:06:25.830 ERROR [CorePan-Analysis-Thread] b.c.jlu.asap.analyses.AnalysisStep : corepan analysis step aborted!
java.io.IOException: abnormal core/pan exit code! exitCode=1
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83)
at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:238)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:250)
at bio.comp.jlu.asap.analyses.CorePanGenomeAnalysis.runStep(CorePanGenomeAnalysis.groovy:118)
at bio.comp.jlu.asap.analyses.CorePanGenomeAnalysis$runStep$1.callCurrent(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at bio.comp.jlu.asap.analyses.PhylogenyAnalysis$runStep$1.callCurrent(Unknown Source)
at bio.comp.jlu.asap.analyses.AnalysisStep.run(AnalysisStep.groovy:79)
2021-07-26 03:06:25.899 INFO [Analyses-Runner-Thread] b.c.jlu.asap.analyses.AnalysisStep : finished pipeline step
2021-07-26 03:07:19.586 INFO [Thread-55] b.comp.jlu.asap.reports.ReportStep : finished corepan report step
2021-07-26 03:07:23.838 INFO [Thread-44] b.comp.jlu.asap.reports.ReportStep : finished help report step
2021-07-26 03:07:28.920 INFO [Thread-56] b.comp.jlu.asap.reports.ReportStep : finished Phylogeny report step
2021-07-26 03:07:29.837 INFO [Thread-49] b.comp.jlu.asap.reports.ReportStep : finished mlst report step
2021-07-26 03:07:33.426 INFO [Thread-51] b.comp.jlu.asap.reports.ReportStep : finished abr report step
2021-07-26 03:07:54.423 INFO [Thread-53] b.comp.jlu.asap.reports.ReportStep : finished mapping report step
2021-07-26 03:07:57.428 ERROR [Thread-43] b.comp.jlu.asap.reports.ReportStep : index reporting step aborted!
java.lang.ArithmeticException: Division undefined
at java.math.BigDecimal.divide(BigDecimal.java:1744)
at org.codehaus.groovy.runtime.typehandling.BigDecimalMath.divideImpl(BigDecimalMath.java:68)
at org.codehaus.groovy.runtime.typehandling.IntegerMath.divideImpl(IntegerMath.java:49)
at org.codehaus.groovy.runtime.dgmimpl.NumberNumberDiv$NumberNumber.invoke(NumberNumberDiv.java:323)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:58)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
at org.codehaus.groovy.runtime.dgmimpl.NumberNumberDiv$DoubleInteger.call(NumberNumberDiv.java:254)
at bio.comp.jlu.asap.reports.IndexReportStep.calcSDev(IndexReportStep.groovy:217)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:157)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:169)
at bio.comp.jlu.asap.reports.IndexReportStep.runStep(IndexReportStep.groovy:164)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at bio.comp.jlu.asap.reports.ReportRunner$runStep$0.callCurrent(Unknown Source)
at bio.comp.jlu.asap.reports.ReportStep.run(ReportStep.groovy:104)
2021-07-26 03:07:58.527 INFO [Thread-52] b.comp.jlu.asap.reports.ReportStep : finished vf report step
2021-07-26 03:08:01.997 INFO [Thread-46] b.comp.jlu.asap.reports.ReportStep : finished taxonomy report step
2021-07-26 03:08:07.001 INFO [Thread-45] b.comp.jlu.asap.reports.ReportStep : finished qc report step
2021-07-26 03:08:14.843 INFO [Thread-47] b.comp.jlu.asap.reports.ReportStep : finished assembly report step
2021-07-26 03:10:47.898 INFO [Thread-50] b.comp.jlu.asap.reports.ReportStep : finished annotation report step
2021-07-26 03:11:14.104 INFO [Thread-48] b.comp.jlu.asap.reports.ReportStep : finished scaffolding report step
2021-07-26 03:11:53.130 INFO [Thread-54] b.comp.jlu.asap.reports.ReportStep : finished snps report step
2021-07-26 03:11:53.147 INFO [Report-Runner-Thread] b.comp.jlu.asap.reports.ReportStep : finished pipeline report step

If it works on conda it'll be more interesting.

I'm running the docker implementation of this program under Ubuntu, getting an error in the ABR step, and I'm not sure where to begin for troubleshooting.

I've attached the (in progress) log file.

asap.log

Do you think there will ever be a bioconda package for asap?

Hi, I requested our school computing center to install ASAP. However, they failed to install it. Below is what they reported.

Following instructions given at

https://github.com/oschwengers/asap#docker

I was trying to build ASA3P singularity container (asa3p.simg) from its docker image hosted at

https://hub.docker.com/r/oschwengers/asap/

The following is the command I used:

singularity build asa3p.simg docker://oschwengers/asap

asa3p.simg was generated. However, ASA3P core scripts were not generated successfully in asa3p.simg. Its asap/asap-docker.sh script can not be found in its container.

I used the -c option to check my configuration input and received this cryptic error. How does one debug this?