RNA-seq --aligner not working - error #10
Comments
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Looking into this.
Does it work if you switch over to HISAT2?
…On Nov 21, 2017 1:31 AM, "dshechter" ***@***.***> wrote:
Just installed cipher, looks really neat and exactly what my group needs
for straightforward analysis. However, I just tried running it for the
first time on a GEO dataset and encountered this odd error, even though I
set the --alinger in the ommand to star (and tried others, non worked):
nextflow run /opt/main.nf --mode rna --config ./path/to/cfog --fasta ./
--gtf /path/to/gtf --lib s --readLen 50 --strandInfo frFirstStrand
--expInfo ./DMSO_exp_config.txt --aligner star --threads 20
N E X T F L O W ~ version 0.25.1
Launching /opt/main.nf [small_easley] - revision: b095c773ef
WARN: Access to undefined parameter analysis -- Initialise it to a
default value eg. params.analysis = some_value
ERROR ~ --aligner should be one of the following: bbmap, bowtie2, bwa,
hisat2, star
-- Check '.nextflow.log' file for details
Nothing helpful in the logs. Any idea? Why isn't it recognizing the flag
chosing star?
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Nevermind, just re-read your post. Very odd. Will get back to you today!
…On Nov 21, 2017 1:31 AM, "dshechter" ***@***.***> wrote:
Just installed cipher, looks really neat and exactly what my group needs
for straightforward analysis. However, I just tried running it for the
first time on a GEO dataset and encountered this odd error, even though I
set the --alinger in the ommand to star (and tried others, non worked):
nextflow run /opt/main.nf --mode rna --config ./path/to/cfog --fasta ./
--gtf /path/to/gtf --lib s --readLen 50 --strandInfo frFirstStrand
--expInfo ./DMSO_exp_config.txt --aligner star --threads 20
N E X T F L O W ~ version 0.25.1
Launching /opt/main.nf [small_easley] - revision: b095c773ef
WARN: Access to undefined parameter analysis -- Initialise it to a
default value eg. params.analysis = some_value
ERROR ~ --aligner should be one of the following: bbmap, bowtie2, bwa,
hisat2, star
-- Check '.nextflow.log' file for details
Nothing helpful in the logs. Any idea? Why isn't it recognizing the flag
chosing star?
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thanks, it's very odd. Happened with the default (no flag) or with any other aligner (including hisat). Here is the .nextflow.log from one I just tried: Nov-21 12:46:06.365 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.25.1 |
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Did you rename the nextflow script from cipher.nf to main.nf as shown in your command line? |
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No - strangely enough that was how it appeared when I cloned the repository. I just deleted it and recloned it and put it in my home dir in case there were some permission issues. FYI now its called cipher.nf. But now it's failing on the fasta file input, which looks fine to me in my command: --fasta /data/NGS/NGS_Data/Stds/hs/GRCh38.fa. It's on a mounted RAID array. Could there be some problems with permissions or something else weird? Here's the new error: |
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Most likely some permission issues, I've run into this problem a few times
on a couple of clusters since moving for my PhD. This has happened with
reference files and even fastq files. Try creating a symlink to your fasta
file on your home directory. If you get a new error (probably the GTF or
something) then this is a permissions error.
…On Tue, Nov 21, 2017 at 10:14 AM, dshechter ***@***.***> wrote:
No - strangely enough that was how it appeared when I cloned the
repository. I just deleted it and recloned it and put it in my home dir in
case there were some permission issues. FYI now its called cipher.nf.
But now it's failing on the fasta file input, which looks fine to me in my
command: --fasta /data/NGS/NGS_Data/Stds/hs/GRCh38.fa. It's on a mounted
RAID array. Could there be some problems with permissions or something else
weird?
Here's the new error:
WARN: Access to undefined parameter fa -- Initialise it to a default
value eg. params.fa = some_value
ERROR ~ Please specify a FASTA file.
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Actually, if that doesn't work you may want to copy the entire fasta file
to your home directory for good measure, just to make sure, I don't know
how symlink handles permissions.
…On Tue, Nov 21, 2017 at 10:38 AM, Carlos Guzman ***@***.***> wrote:
Most likely some permission issues, I've run into this problem a few times
on a couple of clusters since moving for my PhD. This has happened with
reference files and even fastq files. Try creating a symlink to your fasta
file on your home directory. If you get a new error (probably the GTF or
something) then this is a permissions error.
On Tue, Nov 21, 2017 at 10:14 AM, dshechter ***@***.***>
wrote:
> No - strangely enough that was how it appeared when I cloned the
> repository. I just deleted it and recloned it and put it in my home dir in
> case there were some permission issues. FYI now its called cipher.nf.
>
> But now it's failing on the fasta file input, which looks fine to me in
> my command: --fasta /data/NGS/NGS_Data/Stds/hs/GRCh38.fa. It's on a
> mounted RAID array. Could there be some problems with permissions or
> something else weird?
>
> Here's the new error:
> WARN: Access to undefined parameter fa -- Initialise it to a default
> value eg. params.fa = some_value
> ERROR ~ Please specify a FASTA file.
>
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*Bioinformatics & Systems Biology*
University of California, San Diego
*Phone**:* (956) 437-6263
*E-mail*: ***@***.***
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*Bioinformatics & Systems Biology*
University of California, San Diego
*Phone**:* (956) 437-6263
*E-mail*: cag104@ucsd.edu
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I moved everything (data, reference files, cipher directory) to my home directory and I still had an error ('Please specify a FASTA file'). Here are the permissions on the gtf and fa files, within my home directory: -rwxr-xr-x 1 david shechterlab 1.4G Mar 6 2017 GRCh38.83.gtf Any other ideas? I'd really like to use your cipher package, and it would make it easier for my lab members. But no idea how to go forward. Thanks |
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Oh I see what may be going on. The newer version of CIPHER uses --fa
instead of --fasta. Please try running your code as follows:
nextflow run /opt/cipher.nf --mode rna --config <config> --fa <fasta> --gtf
<gtf> --lib s --readLen 50 --strandInfo frFirstStrand --expInfo <expInfo>
--aligner star --threads 20 --subsample --downstream_analysis false
--bamcoverage false
This will give you a minimum testing pass which should let us make sure
that the core functionality of CIPHER is working. If this works then let me
know and we can continue downstream analysis. (Please note that I'm
currently fixing a bug with bamcoverage so for now always run your command
with --bamcoverage false until later today when I push out the fix).
…On Tue, Nov 21, 2017 at 11:58 AM, dshechter ***@***.***> wrote:
I moved everything (data, reference files, cipher directory) to my home
directory and I still had an error ('Please specify a FASTA file'). Here
are the permissions on the gtf and fa files, within my home directory:
-rwxr-xr-x 1 david shechterlab 1.4G Mar 6 2017 GRCh38.83.gtf
-rwxr-xr-x 1 david shechterlab 3.0G Mar 6 2017 GRCh38.fa
Any other ideas? I'd really like to use your cipher package, and it would
make it easier for my lab members. But no idea how to go forward. Thanks
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Thanks - I figured that out myself a few minutes ago after checking the downloaded helpfile. It launched but ended with another error (regardless of directory or running as user or sudo): Launching =============================================== mode: rna subsampled: false clumpify: true threads: 5 aligner: starERROR ~ 3 -- Check script 'cipher.nf' at line: 322 or see '.nextflow.log' file for more details -- Check script 'cipher.nf' at line: 554 or see '.nextflow.log' file for more details |
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Well this is progress I would say lol. Try adding "--clumpify false" to
your command for now. Might as well catch all the errors and fix them at
once.
Thanks for this! It's been a while since I worked on RNA seq data.
…On Nov 21, 2017 12:39 PM, "dshechter" ***@***.***> wrote:
Thanks - I figured that out myself a few minutes ago after checking the
downloaded helpfile. It launched but ended with another error (regardless
of directory or running as user or sudo):
Launching /home/david/cipher-workflow-platform/cipher.nf
[desperate_austin] - revision: d4ab4cbdac
RUN INFORMATION
===============================================
mode: rna
config: /data/NGS/NGS_Data/GEO/X
fasta: /data/NGS/NGS_Data/Stds/hs/X
gtf: /data/NGS/NGS_Data/Stds/hs/X
library: s
read-length: 50
subsampled: false
clumpify: true
bbduk: true
fastqc: true
multiqc: true
mapping: true
bamcoverage: true
downstream_analysis true
threads: 5
aligner: star
ERROR ~ 3
-- Check script 'cipher.nf' at line: 322 or see '.nextflow.log' file for
more details
[warm up] executor > local
ERROR ~ Channel fastqs_s has been used twice as an input by process
clumpify and another operator
-- Check script 'cipher.nf' at line: 554 or see '.nextflow.log' file for
more details
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Glad to help! Would love to have it working. Maybe I'll try a chip-seq dataset as a test also. --clumpify false didn't help... same error. The runtime output is identical to before. The logfile is pretty big, not sure if I should post it here. |
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Go ahead and post it, or add it as an attachment. Could I also get the link
to GEO dataset? The script is working fine on some RNA-seq I took from our
cluster, but it's pair-ended.
Thanks!
…On Tue, Nov 21, 2017 at 12:47 PM, dshechter ***@***.***> wrote:
Glad to help! Would love to have it working. Maybe I'll try a chip-seq
dataset as a test also.
--clumpify false didn't help... same error. The runtime output is
identical to before. The logfile is pretty big, not sure if I should post
it here.
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GSE85107 Here is my cfg file showing the runs I'm mapping: AML2_DMSO AML2_DMSO_rep1 /data/NGS/NGS_Data/GEO/GSE85107_Armstrong2016_AML/fastq/SRR3994142.fastq.gz here's the log: [david@drdisorder fastq]$ more .nextflow.log Nov-21 15:31:03.165 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null |
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Please give it a try now with the command I had previously sent.
…On Tue, Nov 21, 2017 at 1:32 PM, dshechter ***@***.***> wrote:
GSE85107
Here is my cfg file showing the runs I'm mapping:
AML2_DMSO AML2_DMSO_rep1 /data/NGS/NGS_Data/GEO/
GSE85107_Armstrong2016_AML/fastq/SRR3994142.fastq.gz
AML2_DMSO AML2_DMSO_rep2 /data/NGS/NGS_Data/GEO/
GSE85107_Armstrong2016_AML/fastq/SRR3994143.fastq.gz
AML2_DMSO AML2_DMSO_rep3 /data/NGS/NGS_Data/GEO/
GSE85107_Armstrong2016_AML/fastq/SRR3994144.fastq.gz
AML3_DMSO AML3_DMSO_rep1 /data/NGS/NGS_Data/GEO/
GSE85107_Armstrong2016_AML/fastq/SRR3994136.fastq.gz
AML3_DMSO AML3_DMSO_rep2 /data/NGS/NGS_Data/GEO/
GSE85107_Armstrong2016_AML/fastq/SRR3994137.fastq.gz
AML3_DMSO AML3_DMSO_rep3 /data/NGS/NGS_Data/GEO/
GSE85107_Armstrong2016_AML/fastq/SRR3994138.fastq.gz
here's the log:
***@***.*** fastq]$ more .nextflow.log
Nov-21 15:31:00.712 [main] DEBUG nextflow.cli.Launcher - $>
/home/david/anaconda2/bin/nextflow run /home/david/cipher-workflow-
platform/cipher.nf --mode rna --config /data/NGS/NGS_Data/GEO/
GSE85107_Armstrong2016_AML/fastq/AML2_AML3_DMSO-cipher.cfg --fa /data/NGS
/NGS_Data/Stds/hs/GRch38.fa --gtf /data/NGS/NGS_Data/Stds/hs/Homo_sapiens.GRCh38.83.gtf
--lib s --readLen 50 --strandInfo frFirstStrand --expInfo
/data/NGS/NGS_Data/GEO/GSE85107_Armstrong2016_AML/fastq/DMSO_exp_config.txt
--aligner star --threads 5
Nov-21 15:31:00.810 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~
version 0.25.1
Nov-21 15:31:00.834 [main] INFO nextflow.cli.CmdRun - Launching
/home/david/cipher-workflow-platform/cipher.nf [desperate_austin] -
revision: d4ab4cbdac
Nov-21 15:31:00.844 [main] DEBUG nextflow.config.ConfigBuilder - Found
config base: /home/david/cipher-workflow-platform/nextflow.config
Nov-21 15:31:00.845 [main] DEBUG nextflow.config.ConfigBuilder - Parsing
config file: /home/david/cipher-workflow-platform/nextflow.config
Nov-21 15:31:01.098 [main] DEBUG nextflow.config.ConfigBuilder - Setting
config profile: 'standard'
Nov-21 15:31:01.160 [main] DEBUG nextflow.Session - Session uuid:
ac5c1ccb-ecfb-4129-b00a-ad3d3f6fcee6
Nov-21 15:31:01.160 [main] DEBUG nextflow.Session - Run name:
desperate_austin
Nov-21 15:31:01.162 [main] DEBUG nextflow.Session - Executor pool size: 40
Nov-21 15:31:01.178 [main] DEBUG nextflow.cli.CmdRun -
Version: 0.25.1 build 4460
Modified: 27-06-2017 12:31 UTC (08:31 EDT)
System: Linux 3.10.0-514.26.2.el7.x86_64
Runtime: Groovy 2.4.11 on OpenJDK 64-Bit Server VM 1.8.0_151-b12
Encoding: UTF-8 (UTF-8)
Process: ***@***.*** [10.49.65.147]
CPUs: 40 - Mem: 125.6 GB (756.9 MB) - Swap: 6 GB (6 GB)
Nov-21 15:31:01.209 [main] DEBUG nextflow.Session - Work-dir:
/mnt/raid/NGS/NGS_Data/GEO/GSE85107_Armstrong2016_AML/fastq/work
[ext2/ext3]
Nov-21 15:31:01.356 [main] DEBUG nextflow.Session - Session start invoked
Nov-21 15:31:01.359 [main] DEBUG nextflow.processor.TaskDispatcher -
Dispatcher > start
Nov-21 15:31:01.360 [main] DEBUG nextflow.script.ScriptRunner - > Script
parsing
Nov-21 15:31:03.016 [main] DEBUG nextflow.script.ScriptRunner - >
Launching execution
Nov-21 15:31:03.044 [main] INFO nextflow.Nextflow -
Nov-21 15:31:03.044 [main] INFO nextflow.Nextflow - RUN INFORMATION
Nov-21 15:31:03.044 [main] INFO nextflow.Nextflow -
===============================================
Nov-21 15:31:03.044 [main] INFO nextflow.Nextflow -
Nov-21 15:31:03.045 [main] INFO nextflow.Nextflow - mode: rna
Nov-21 15:31:03.045 [main] INFO nextflow.Nextflow - config:
/data/NGS/NGS_Data/GEO/GSE85107_Armstrong2016_AML/
fastq/AML2_AML3_DMSO-cipher.cfg
Nov-21 15:31:03.045 [main] INFO nextflow.Nextflow - fasta:
/data/NGS/NGS_Data/Stds/hs/GRch38.fa
Nov-21 15:31:03.045 [main] INFO nextflow.Nextflow - gtf:
/data/NGS/NGS_Data/Stds/hs/Homo_sapiens.GRCh38.83.gtf
Nov-21 15:31:03.045 [main] INFO nextflow.Nextflow - library: s
Nov-21 15:31:03.045 [main] INFO nextflow.Nextflow - read-length: 50
Nov-21 15:31:03.045 [main] INFO nextflow.Nextflow -
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow - subsampled: false
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow -
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow - clumpify: true
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow - bbduk: true
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow - fastqc: true
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow - multiqc: true
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow - mapping: true
Nov-21 15:31:03.046 [main] INFO nextflow.Nextflow - bamcoverage: true
Nov-21 15:31:03.047 [main] INFO nextflow.Nextflow - downstream_analysis
true
Nov-21 15:31:03.047 [main] INFO nextflow.Nextflow -
Nov-21 15:31:03.047 [main] INFO nextflow.Nextflow - threads: 5
Nov-21 15:31:03.047 [main] INFO nextflow.Nextflow -
Nov-21 15:31:03.047 [main] INFO nextflow.Nextflow - aligner: star
Nov-21 15:31:03.047 [main] INFO nextflow.Nextflow -
===============================================
Nov-21 15:31:03.047 [main] INFO nextflow.Nextflow -
Nov-21 15:31:03.118 [Actor Thread 1] ERROR n.extension.DataflowExtensions
- @unknown <https://github.com/unknown>
java.lang.ArrayIndexOutOfBoundsException: 3
at org.codehaus.groovy.runtime.dgmimpl.arrays.ObjectArrayGetAtMetaMethod.
invoke(ObjectArrayGetAtMetaMethod.java:41)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.
invoke(PojoMetaMethodSite.java:51)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.
call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.
defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
call(AbstractCallSite.java:125)
at _nf_script_cc617d25$_run_closure1.doCall(_nf_script_cc617d25:322)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.
invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.
call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.
defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
call(AbstractCallSite.java:125)
at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:50)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.
invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(
DataflowOperatorActor.java:120)
at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(
DataflowOperatorActor.java:108)
at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMes
sages(AbstractLoopingActor.java:293)
at groovyx.gpars.actor.AbstractLoopingActor.access$
400(AbstractLoopingActor.java:30)
at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(
AbstractLoopingActor.java:93)
at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
at java.util.concurrent.ThreadPoolExecutor.runWorker(
ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(
ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Nov-21 15:31:03.133 [Actor Thread 1] DEBUG nextflow.Session - Session
aborted -- Cause: 3
Nov-21 15:31:03.164 [Actor Thread 1] DEBUG nextflow.Session - The
following nodes are still active:
[operator] map
Nov-21 15:31:03.165 [main] DEBUG nextflow.processor.ProcessFactory - <<
taskConfig executor: null
Nov-21 15:31:03.165 [main] DEBUG nextflow.processor.ProcessFactory - >>
processorType: 'local'
Nov-21 15:31:03.171 [main] DEBUG nextflow.executor.Executor - Initializing
executor: local
Nov-21 15:31:03.172 [main] INFO nextflow.executor.Executor - [warm up]
executor > local
Nov-21 15:31:03.177 [main] DEBUG n.processor.LocalPollingMonitor -
Creating local task monitor for executor 'local' > cpus=40; memory=125.6
GB; capacity=40; pollInterval=100ms; dumpInterval=5m
Nov-21 15:31:03.181 [main] DEBUG nextflow.processor.TaskDispatcher -
Starting monitor: LocalPollingMonitor
Nov-21 15:31:03.182 [main] DEBUG n.processor.TaskPollingMonitor - >>>
barrier register (monitor: local)
Nov-21 15:31:03.184 [main] DEBUG nextflow.executor.Executor - Invoke
register for executor: local
Nov-21 15:31:03.189 [Task monitor] DEBUG n.processor.TaskPollingMonitor -
<<< barrier arrives (monitor: local)
Nov-21 15:31:03.215 [main] DEBUG nextflow.Session - >>> barrier register
(process: fetch_chrom_sizes)
Nov-21 15:31:03.226 [main] DEBUG nextflow.processor.TaskProcessor -
Creating operator > fetch_chrom_sizes -- maxForks: 40
Nov-21 15:31:03.252 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor
- <fetch_chrom_sizes> Poison pill arrived; port: 1
Nov-21 15:31:03.253 [main] DEBUG nextflow.processor.ProcessFactory - <<
taskConfig executor: null
Nov-21 15:31:03.253 [main] DEBUG nextflow.processor.ProcessFactory - >>
processorType: 'local'
Nov-21 15:31:03.254 [main] DEBUG nextflow.executor.Executor - Initializing
executor: local
Nov-21 15:31:03.255 [Actor Thread 2] DEBUG nextflow.processor.StateObj -
<fetch_chrom_sizes> State before poison: StateObj[submitted: 1; completed:
0; poisoned: false ]
Nov-21 15:31:03.255 [main] DEBUG nextflow.Session - >>> barrier register
(process: create_mapping_index)
Nov-21 15:31:03.263 [main] DEBUG nextflow.processor.TaskProcessor -
Creating operator > create_mapping_index -- maxForks: 40
Nov-21 15:31:03.268 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor
- <create_mapping_index> Poison pill arrived; port: 2
Nov-21 15:31:03.268 [Actor Thread 2] DEBUG nextflow.processor.StateObj -
<create_mapping_index> State before poison: StateObj[submitted: 1;
completed: 0; poisoned: false ]
Nov-21 15:31:03.297 [main] DEBUG nextflow.processor.ProcessFactory - <<
taskConfig executor: null
Nov-21 15:31:03.298 [main] DEBUG nextflow.processor.ProcessFactory - >>
processorType: 'local'
Nov-21 15:31:03.298 [main] DEBUG nextflow.executor.Executor - Initializing
executor: local
Nov-21 15:31:03.300 [main] DEBUG nextflow.Session - >>> barrier register
(process: clumpify)
Nov-21 15:31:03.310 [main] DEBUG nextflow.processor.TaskProcessor -
Creating operator > clumpify -- maxForks: 40
Nov-21 15:31:03.323 [Actor Thread 3] DEBUG nextflow.util.CacheHelper -
Unable to hash file: /data/NGS/NGS_Data/Stds/hs/GRch38.fa -- Cause:
java.nio.file.NoSuchFileException: /data/NGS/NGS_Data/Stds/hs/GRch38.fa
Nov-21 15:31:03.439 [main] ERROR nextflow.cli.Launcher - @unknown
<https://github.com/unknown>
nextflow.dag.MultipleInputChannelException: Channel fastqs_s has been
used twice as an input by process clumpify and another operator
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.runtime.callsite.ConstructorSite$
ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.
defaultCallConstructor(CallSiteArray.java:60)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(
AbstractCallSite.java:235)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(
AbstractCallSite.java:263)
at nextflow.dag.DAG.inbound(DAG.groovy:192)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.
invokeMethod(ClosureMetaClass.java:384)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.
callCurrent(PogoMetaClassSite.java:69)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
callCurrent(AbstractCallSite.java:174)
at nextflow.dag.DAG$_addVertex_closure1.doCall(DAG.groovy:131)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.
invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(
DefaultGroovyMethods.java:2040)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(
DefaultGroovyMethods.java:2025)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(
DefaultGroovyMethods.java:2066)
at org.codehaus.groovy.runtime.dgm$162.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$
PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.
call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
callSafe(AbstractCallSite.java:87)
at nextflow.dag.DAG.addVertex(DAG.groovy:130)
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 nextflow.dag.DAG.addProcessNode(DAG.groovy:89)
at nextflow.dag.NodeMarker.addProcessNode(NodeMarker.groovy:33)
at nextflow.dag.NodeMarker$addProcessNode$2.call(Unknown Source)
at nextflow.processor.TaskProcessor.createOperator(
TaskProcessor.groovy:484)
at nextflow.processor.TaskProcessor.run(TaskProcessor.groovy:378)
at nextflow.processor.TaskProcessor$run.call(Unknown Source)
at nextflow.script.BaseScript.process(BaseScript.groovy:134)
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:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.
callCurrent(AbstractCallSite.java:174)
at _nf_script_cc617d25.run(_nf_script_cc617d25:554)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:325)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:156)
at nextflow.cli.CmdRun.run(CmdRun.groovy:223)
at nextflow.cli.Launcher.run(Launcher.groovy:410)
at nextflow.cli.Launcher.main(Launcher.groovy:564)
Nov-21 15:31:03.440 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor
- <create_mapping_index> After stop
—
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*Bioinformatics & Systems Biology*
University of California, San Diego
*Phone**:* (956) 437-6263
*E-mail*: cag104@ucsd.edu
|
|
updated the local git clone, still failed but at a different line. I'm heading out shortly but can try more tomorrow. Thanks! Launching =============================================== mode: rna subsampled: true clumpify: true threads: 20 aligner: starERROR ~ 3 -- Check script 'cipher.nf' at line: 323 or see '.nextflow.log' file for more details -- Check script 'cipher.nf' at line: 347 or see '.nextflow.log' file for more details |
|
Tried a test with some inhouse Chipseq data and ended with the same error: [david@drdisorder fq]$ nextflow run ~/cipher-workflow-platform/cipher.nf --mode chip --config ./cipher.cfg --fa /data/NGS/NGS_Data/Stds/GRCh38.fa --gtf /data/NGS/NGS_Data/Stds/hs/Homo_sapiens.GRCh38.83.gtf --lib s --readLen 150 --threads 30 --subsample --downstream_analysis false --clumpify false --bamcoverage false =============================================== mode: chip subsampled: true clumpify: false threads: 30 aligner: bbmapERROR ~ 0 -- Check script 'cipher.nf' at line: 320 or see '.nextflow.log' file for more details -- Check script 'cipher.nf' at line: 347 or see '.nextflow.log' file for more details |
|
That's really wierd. On my system, everything works out fine and this issue
doesn't come up. What version of Nextflow are you using?
…On Nov 21, 2017 8:04 PM, "dshechter" ***@***.***> wrote:
Tried a test with some inhouse Chipseq data and ended with the same error:
***@***.*** fq]$ nextflow run ~/cipher-workflow-platform/cipher.nf
--mode chip --config ./cipher.cfg --fa /data/NGS/NGS_Data/Stds/GRCh38.fa
--gtf /data/NGS/NGS_Data/Stds/hs/Homo_sapiens.GRCh38.83.gtf --lib s
--readLen 150 --threads 30 --subsample --downstream_analysis false
--clumpify false --bamcoverage false
N E X T F L O W ~ version 0.25.1
Launching /home/david/cipher-workflow-platform/cipher.nf [zen_spence] -
revision: a66dfdd7aa
RUN INFORMATION
===============================================
mode: chip
config: /mnt/raid/NGS/NGS_Data/J153+J634/fq/cipher.cfg
fasta: /data/NGS/NGS_Data/Stds/GRCh38.fa
gtf: /data/NGS/NGS_Data/Stds/hs/Homo_sapiens.GRCh38.83.gtf
library: s
read-length: 150
subsampled: true
clumpify: false
bbduk: true
fastqc: true
multiqc: true
mapping: true
bamcoverage: false
downstream_analysis false
threads: 30
aligner: bbmap
ERROR ~ 0
-- Check script 'cipher.nf' at line: 320 or see '.nextflow.log' file for
more details
[warm up] executor > local
ERROR ~ Channel fastqs_s has been used twice as an input by process
subsample and another operator
-- Check script 'cipher.nf' at line: 347 or see '.nextflow.log' file for
more details
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$ conda list |grep nextflow I think that's the latest version in bioconda. |
|
I can't reproduce your error with either RNA-seq or ChIP-seq data on my computer or my cluster, and some other people in my lab are running this fine. Can you try running this on a personal computer/laptop using the example data in the cipher example_data folder? |
|
I downloaded nextflow 0.26.4733 independently of conda. Tried running the script and now have some new errors (below). Maybe you are running an earlier version? N E X T F L O W ~ version 0.26.1 =============================================== mode: rna subsampled: true clumpify: true threads: 5 aligner: starERROR ~ 3 -- Check script 'cipher.nf' at line: 323 or see '.nextflow.log' file for more details Workflow completed on: Wed Nov 22 12:45:30 EST 2017 Submit issues/requests on GitHub or e-mail cag104@ucsd.edu |
|
I tried it on a small ubuntu VM, but not enough storage space to get everything local. On my main server, I finally got the example chip data running by eliminating any directory symbolic links in the config file (e.g. went from /data to /mnt/raid/). However that didn't work with the RNA-seq pipeline. I'll keep playing with it! Thanks, must be something along these lines that would make it a machine specific problem. |
|
Ha - figured it out. You have the RNA-seq script asking for chip-seq annotations in the config file. See lines 323-325 in cipher.nf. For now I added dummy text to the config file, and with explicit path naming it seems to work... |
|
WOW. I will fix this asap.
Thanks a ton for catching this!
…On Wed, Nov 22, 2017 at 11:20 AM, dshechter ***@***.***> wrote:
Ha - figured it out. You have the RNA-seq script asking for chip-seq
annotations in the config file. See lines 323-325 in cipher.nf. For now I
added dummy text to the config file, and with explicit path naming it seems
to work...
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--
*Carlos Guzman - Graduate Student*
*Bioinformatics & Systems Biology*
University of California, San Diego
*Phone**:* (956) 437-6263
*E-mail*: cag104@ucsd.edu
|
|
Easiest fix was leaving single ended config at 5 columns and pair ended configs at 6 columns. Will update README. |
Just installed cipher, looks really neat and exactly what my group needs for straightforward analysis. However, I just tried running it for the first time on a GEO dataset and encountered this odd error, even though I set the --alinger in the ommand to star (and tried others, non worked):
nextflow run /opt/main.nf --mode rna --config ./path/to/cfog --fasta ./ --gtf /path/to/gtf --lib s --readLen 50 --strandInfo frFirstStrand --expInfo ./DMSO_exp_config.txt --aligner star --threads 20
N E X T F L O W ~ version 0.25.1
Launching
/opt/main.nf[small_easley] - revision: b095c773efWARN: Access to undefined parameter
analysis-- Initialise it to a default value eg.params.analysis = some_valueERROR ~ --aligner should be one of the following: bbmap, bowtie2, bwa, hisat2, star
-- Check '.nextflow.log' file for details
Nothing helpful in the logs. Any idea? Why isn't it recognizing the flag chosing star?
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