Multiple bugs in conda drop - mae pipeline #104
Comments
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Dear @gevro sorry for those issues. We did test it on bioconda and it went through. Both of the rules without issues. Could you post your conda environment at the installed versions? Apparently this is a known issue. Could you try to set the channels into the right order if not already tried? You should not need the default channel. If this solved your problem we will updated it on our readme. Regarding the second error @vyepez88 can probably say more about it. |
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Thanks. I'm not sure I understand. What do you need to me to do? |
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Here is my conda environment details. Also, my channels are correct. So this must be a bug in your conda package. (/gpfs/home/evrong01/bin/drop_conda) [evrong01@bigpurple-ln3 ~]$ conda list packages in environment at /gpfs/home/evrong01/bin/drop_conda:Name Version Build Channel_libgcc_mutex 0.1 conda_forge conda-forge
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To fix the samtools issue probably requires upgrading to samtools 1.9. But doing this would affect other packages that might mess up DROP. Can you let me know the correct fix for this and fix the drop conda packages so that everything is working properly? (/gpfs/home/evrong01/bin/drop_conda) [evrong01@bigpurple-ln3 ~]$ conda install -c bioconda samtools=1.9 ==> WARNING: A newer version of conda exists. <== Please update conda by running Package Planenvironment location: /gpfs/home/evrong01/evronylab/bin/drop_conda added / updated specs: The following packages will be downloaded: The following packages will be UPDATED: openssl 1.1.1g-h516909a_0 --> 1.1.1g-h516909a_1 The following packages will be DOWNGRADED: bcftools 1.10.2-h4f4756c_3 --> 1.8-h4da6232_3 |
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@gevro you basically have now the solution by upgrading the samtool version. The only big differences where the three packages I issued an issue on bioconda on why this happend in the first place and how to solve it. As I do not know how to enforce this without fixing every single package version, which is not the idea of conda/bioconda. @mumichae or @vyepez88 can you please make a FAQ and add this command to it as long as it is not fixed by conda/bioconda. |
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Hi, regarding your 3rd error |
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When will be the next release? |
Hi,
The 'mae' pipeline still has multiple bugs. I thought the conda environment was tested and working.
See below. Can you please fix these?
rule create_SNVs:
input: /gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/resource/chr_NCBI_UCSC.txt, /gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/resource/chr_UCSC_NCBI.txt, /gpfs/data/variants/UDP-1000/WES.SNVINDEL/UDP-1002_exome.vcf.gz, /gpfs/scratch/evrong01/UDP-RNA_seq/UDP-1002_RNA.bam, /gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/Scripts/MAE/filterSNVs.sh
output: /gpfs/scratch/evrong01/droptest2/root/processed_data/mae/snvs/1841999--UDP-1002_RNA.vcf.gz, /gpfs/scratch/evrong01/droptest2/root/processed_data/mae/snvs/1841999--UDP-1002_RNA.vcf.gz.tbi
jobid: 32
wildcards: vcf=1841999, rna=UDP-1002_RNA
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
rule Scripts_MAE_gene_name_mapping_R:
input: /gpfs/data/reference-files/GRCh38_gencode-STAR/gencode.v32.primary_assembly.annotation.gtf, Scripts/MAE/ge
ne_name_mapping.R
output: /gpfs/scratch/evrong01/droptest2/root/processed_data/mae/gene_name_mapping_v32.tsv
jobid: 14
wildcards: annotation=v32
INFO 2020-08-02 12:24:55 CreateSequenceDictionary Output dictionary will be written in /gpfs/data/refer
ence-files/GRCh38_gencode-STAR/GRCh38.primary_assembly.genome.dict
12:24:55.253 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/bin/drop_conda/share/
gatk4-4.1.8.1-0/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Sun Aug 02 12:24:55 EDT 2020] CreateSequenceDictionary --REFERENCE /gpfs/data/reference-files/GRCh38_gencode-STAR/GR
Ch38.primary_assembly.genome.fa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false -
-VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --
GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INF
LATER false
[Sun Aug 02 12:24:55 EDT 2020] Executing as evrong01@cn-0020 on Linux 3.10.0-693.17.1.el7.x86_64 amd64; OpenJDK 64-Bit Server V
M 1.8.0_192-b01; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.8.1
[Sun Aug 02 12:24:55 EDT 2020] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2326265856
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
picard.PicardException: /gpfs/data/reference-files/GRCh38_gencode-STAR/GRCh38.primary_assembly.genome.dict already ex
ists. Delete this file and try again, or specify a different output file.
at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:220)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor
:
.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /gpfs/data/bin/drop_conda/share/gatk4-4.1.8.1-0/gatk-package-4.1.8.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gpfs/data/bin/drop_conda/share/gatk4-4.1.8.1-0/gatk-package-4.1.8.1-local.jar CreateSequenceDictionary --REFERENCE /gpfs/data/reference-files/GRCh38_gencode-STAR/GRCh38.primary_assembly.genome.fa
[Sun Aug 2 12:24:56 2020]
Error in rule create_dict:
jobid: 31
output: /gpfs/data/reference-files/GRCh38_gencode-STAR/GRCh38.dict
shell:
gatk CreateSequenceDictionary --REFERENCE /gpfs/data/reference-files/GRCh38_gencode-STAR/GRCh38.primary_assembly.genome.fa
(exited with non-zero exit code)
object 'gene_status' not found
Calls: [ -> [.data.table -> eval -> eval
Execution halted
[Sun Aug 2 12:25:53 2020]
Error in rule Scripts_MAE_gene_name_mapping_R:
jobid: 14
output: /gpfs/scratch/evrong01/droptest2/root/processed_data/mae/gene_name_mapping_v32.tsv
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