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Oshlack / ALLSorts

ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.
MIT License
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Unable to run the automated pipeline with fastq files #13

Open ChengHsiangLu opened 2 years ago

ChengHsiangLu commented 2 years ago

Hi, I'm new to the bioinformatics field and I encountered errors that I don't know how to solve it. I've followed the Installation steps and run the test successfully. https://github.com/Oshlack/ALLSorts/wiki/1.-Installation

I've also. installed Bpipe, STAR, and samtools. Then, I set environmental variables for executables.

However, when I tried to follow the automated pipeline starting with FASTQ files and put two fastq.gz files in /home/ec2-user/ALLSorts/tests/fastq/ directory, it showed errors. This is the code I used:

"(allsorts) [ec2-user@ip-10-242-22-113 ALLSorts]$ bpipe -p results=/data/ALLSorts_new/test_results -p threads=16 -p amem=122000000000 -p type="fastq" -p strand="no" -p format="/%.fastq.gz" -p genome_dir="/data/ALLSorts_new/ALLSorts_files" /data/ALLSorts_new/ALLSorts/tools/counts/counts.groovy /home/ec2-user/ALLSorts/tests/fastq/*.fastq.gz"

MSG: vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv MSG: NOTE: Pipeline completed as process 18958. Trailing lines follow. MSG: Use bpipe log -n to see more lines MSG: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

╒══════════════════════════════════════════════════════════════════════════════════════════════════╕ | Starting Pipeline at 2022-09-22 23:50 | ╘══════════════════════════════════════════════════════════════════════════════════════════════════╛

========================================== Stage make_dir ========================================== WARNING: An error occurred evaluating your pipeline stage: groovy.lang.MissingPropertyException: No such property: single in stage make_dir. Please see Bpipe log file for full details. =========================================== Bpipe Error ============================================

An error occurred executing your pipeline:

                         No such property: single in stage make_dir

Please see the details below for more information.

========================================== Error Details ===========================================

groovy.lang.MissingPropertyException: No such property: single in stage make_dir at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at counts.groovy$_run_closure1$_closure10.doCall(counts.groovy:90) at counts.groovy$_run_closure1$_closure10.doCall(counts.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at counts.groovy$_run_closure1.doCall(counts.groovy:89) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at counts.groovy.run(counts.groovy:192) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

====================================================================================================

More details about why this error occurred may be available in the full log file .bpipe/bpipe.log

I found someone who had a similar issue to this. https://github.com/Oshlack/Slinker/issues/2

Nevertheless, I reinstalled everything and tried but still got this error message. What can I do to solve this error? Thank you.

Best, Sam

norberto-sanchez commented 1 year ago

Did you resolve the error? I am trying to run the algorithm but I have the same issue.