PostprocessGermlineCNVCalls returns error for sample_name.txt file
REQUIRED for all errors and issues:
a) GATK version used: 4.3.0.0 (same error in 4.2.0.0 as well)
b) Exact command used:
gatk PostprocessGermlineCNVCalls --calls-shard-path data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller/S29_germlinecnvcaller-calls --model-shard-path path/hg38_acnv_models/model_name/cnv_model/model --sample-index 0 --autosomal-ref-copy-number 2 --allosomal-contig chrX --allosomal-contig chrY --contig-ploidy-calls data/cnv/gatk_cnv/S29_determine_ploidy/S29_determine_ploidy-calls --output-genotyped-intervals data/cnv/gatk_cnv/cnv_call/S29_genotyped_intervals_gatk_cnv.vcf --output-genotyped-segments data/cnv/gatk_cnv/cnv_call/S29_genotyped_segments_gatk_cnv.vcf --output-denoised-copy-ratios data/cnv/gatk_cnv/cnv_call/S29_genotyped_denoised_copy_ratios_gatk_cnv.vcf
Using GATK jar /home/hatice/miniconda3/envs/gatk/share/gatk4-4.2.0.0-1/gatk-package-4.2.0.0-local.jar
c) Entire program log:
gatk PostprocessGermlineCNVCalls --calls-shard-path data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller/S29_germlinecnvcaller-calls --model-shard-path path/hg38_acnv_models/model_name/cnv_model/model --sample-index 0 --autosomal-ref-copy-number 2 --allosomal-contig chrX --allosomal-contig chrY --contig-ploidy-calls data/cnv/gatk_cnv/S29_determine_ploidy/S29_determine_ploidy-calls --output-genotyped-intervals data/cnv/gatk_cnv/cnv_call/S29_genotyped_intervals_gatk_cnv.vcf --output-genotyped-segments data/cnv/gatk_cnv/cnv_call/S29_genotyped_segments_gatk_cnv.vcf --output-denoised-copy-ratios data/cnv/gatk_cnv/cnv_call/S29_genotyped_denoised_copy_ratios_gatk_cnv.vcf
Using GATK jar /home/hatice/miniconda3/envs/gatk/share/gatk4-4.2.0.0-1/gatk-package-4.2.0.0-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 /home/hatice/miniconda3/envs/gatk/share/gatk4-4.2.0.0-1/gatk-package-4.2.0.0-local.jar PostprocessGermlineCNVCalls --calls-shard-path data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller/S29_germlinecnvcaller-calls --model-shard-path path/hg38_acnv_models/model_name/cnv_model/model --sample-index 0 --autosomal-ref-copy-number 2 --allosomal-contig chrX --allosomal-contig chrY --contig-ploidy-calls data/cnv/gatk_cnv/S29_determine_ploidy/S29_determine_ploidy-calls --output-genotyped-intervals data/cnv/gatk_cnv/cnv_call/S29_genotyped_intervals_gatk_cnv.vcf --output-genotyped-segments data/cnv/gatk_cnv/cnv_call/S29_genotyped_segments_gatk_cnv.vcf --output-denoised-copy-ratios data/cnv/gatk_cnv/cnv_call/S29_genotyped_denoised_copy_ratios_gatk_cnv.vcf
16:56:59.433 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/hatice/miniconda3/envs/gatk/share/gatk4-4.2.0.0-1/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jan 06, 2025 4:56:59 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:56:59.547 INFO PostprocessGermlineCNVCalls - ------------------------------------------------------------
16:56:59.547 INFO PostprocessGermlineCNVCalls - The Genome Analysis Toolkit (GATK) v4.2.0.0
16:56:59.547 INFO PostprocessGermlineCNVCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
16:56:59.547 INFO PostprocessGermlineCNVCalls - Executing as hatice@hatice on Linux v6.8.0-51-generic amd64
16:56:59.547 INFO PostprocessGermlineCNVCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_412-b08
16:56:59.547 INFO PostprocessGermlineCNVCalls - Start Date/Time: January 6, 2025 4:56:59 PM TRT
16:56:59.547 INFO PostprocessGermlineCNVCalls - ------------------------------------------------------------
16:56:59.547 INFO PostprocessGermlineCNVCalls - ------------------------------------------------------------
16:56:59.547 INFO PostprocessGermlineCNVCalls - HTSJDK Version: 2.24.0
16:56:59.547 INFO PostprocessGermlineCNVCalls - Picard Version: 2.25.0
16:56:59.547 INFO PostprocessGermlineCNVCalls - Built for Spark Version: 2.4.5
16:56:59.547 INFO PostprocessGermlineCNVCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:56:59.547 INFO PostprocessGermlineCNVCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:56:59.547 INFO PostprocessGermlineCNVCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:56:59.547 INFO PostprocessGermlineCNVCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:56:59.547 INFO PostprocessGermlineCNVCalls - Deflater: IntelDeflater
16:56:59.547 INFO PostprocessGermlineCNVCalls - Inflater: IntelInflater
16:56:59.547 INFO PostprocessGermlineCNVCalls - GCS max retries/reopens: 20
16:56:59.547 INFO PostprocessGermlineCNVCalls - Requester pays: disabled
16:56:59.547 INFO PostprocessGermlineCNVCalls - Initializing engine
16:57:01.700 INFO PostprocessGermlineCNVCalls - Done initializing engine
16:57:01.925 INFO PostprocessGermlineCNVCalls - Shutting down engine
[January 6, 2025 4:57:01 PM TRT] org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=2331508736
***********************************************************************
A USER ERROR has occurred: Bad input: Could not read the sample name text file at /home/hatice/Desktop/Pipelines/bioinformatics_team/massive_analyser/single_sample/data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller/S29_germlinecnvcaller-calls/SAMPLE_0/sample_name.txt.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
The error which I pasted above is because the sample_name.txt file (which is generated in the previous step of the germline CNV caller pipeline using GATK's DetermineGermlineContigPloidy tool that outputs a folder within folders (S29_determine_ploidy/S29_determine_ploidy-calls/SAMPLE_0) that contains contig_ploidy.tsv, global_read_depthçtsv, mu_psi_s_log__.tsv, sample_name.txt and std_psi_s_log__.tsv files. This folder is directly given to the PostprocessGermlineCNVCalls tool with the --contig-ploidy-calls parameter as "--contig-ploidy-calls data/cnv/gatk_cnv/S29_determine_ploidy/S29_determine_ploidy-calls" however, as shown in the tool's output the PostprocessGermlineCNVCalls tool looks for the sample_name.txt in a different folder generated by GermlineCNVCaller tool (data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller/S29_germlinecnvcaller-calls). But this tool does not output the sample_name.txt file as an output, so why does the PostprocessGermlineCNVCalls tool look for it in there?
-
Can you check to see if your previous step completed successfully? I am checking a run that I have and looks like both tools create a sample_name.txt file in their respective sample folders. Top folder is from DetermineGermlineContigPloidy and bottom is from GermlineCNVCaller.
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Hi, thank you for your quick response.
You are right, the output files for GATK GermlineCNVCaller tool are missing (for some reason it did not generate an error in the pipeline). Here is the truncated log file (It is very long since the sequence contig dictionary output logs, but I am pasting the error part):
OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://www.intel.com/software/products/support/.
13:15:51.597 INFO GermlineCNVCaller - Shutting down engine
[January 7, 2025 at 1:15:51 PM TRT] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=2109734912
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 134
Command Line: python /tmp/case_denoising_calling.10730251279194866594.py --ploidy_calls_path=/data/cnv/gatk_cnv/S29_determine_ploidy/S29_determine_ploidy-calls --output_calls_path=/data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller/S29_germlinecnvcaller-calls --output_tracking_path=/data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller/S29_germlinecnvcaller-tracking --input_model_path=/home/hatice/workstation/dbs4_7_dev/hg38_acnv_models/roche_4100_ces/cnv_model/model --random_seed=1984 --read_count_tsv_files /tmp/S29.rc17585420808102314807.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --num_samples_copy_ratio_approx=200 --p_alt=1.000000e-06 --cnv_coherence_length=1.000000e+04 --max_copy_number=5 --learning_rate=1.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.900000e-01 --log_emission_samples_per_round=50 --log_emission_sampling_rounds=10 --log_emission_sampling_median_rel_error=5.000000e-03 --max_advi_iter_first_epoch=5000 --max_advi_iter_subsequent_epochs=200 --min_training_epochs=10 --max_training_epochs=50 --initial_temperature=1.500000e+00 --num_thermal_advi_iters=2500 --convergence_snr_averaging_window=500 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=10 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=1.000000e+00 --disable_caller=false --disable_sampler=false --disable_annealing=false
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:351)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
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 /.snakemake/conda/60afddbf3477410829bf5ec83a45f5fc_/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-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 /.snakemake/conda/60afddbf3477410829bf5ec83a45f5fc_/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar GermlineCNVCaller --run-mode CASE -I data/cnv/gatk_cnv/collect_read_counts/S29.tsv --contig-ploidy-calls data/cnv/gatk_cnv/S29_determine_ploidy/S29_determine_ploidy-calls --model /hg38_acnv_models/roche_4100_ces/cnv_model/model --output data/cnv/gatk_cnv/cnv_raw/S29_germlinecnvcaller --output-prefix S29_germlinecnvcaller --verbosity DEBUG2025-01-07 13:15 INFO: Germline CNV caller step completed!
Apparently, this is a python error but gcnvkernel 0.8 requires python 3.6.10, but there is a script error. What do you suggest?
-
Hi again.
There is a python exit code 134 which means SIGABRT issued by the system due to library links. This is probably due to misaligned dependencies in the conda environment of yours. We do not recommend using conda to directly install gatk environment maintained in repositories but manually installing our conda environment using the command below.
First obtain an updated conda installation /or install miniconda from scratch
conda update conda
Then use the below command using the yml file from our zipped distribution file
conda env create -f gatkcondaenv.yml
Other means of creating this environment usually ends up installing incorrect/misaligned dependencies that results in such errors.
Below is the list of installed dependencies in this environment for version 4.6.0.0 (which still uses python 3.6 and theano)
# packages in environment at /opt/miniconda/envs/gatk:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
_tflow_select 2.3.0 mkl
absl-py 0.15.0 pyhd8ed1ab_0 conda-forge
astor 0.8.1 pyh9f0ad1d_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_33 conda-forge
biopython 1.76 py36h516909a_0 conda-forge
blas 1.1 openblas conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
ca-certificates 2024.6.2 hbcca054_0 conda-forge
cairo 1.16.0 hcf35c78_1003 conda-forge
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
curl 7.68.0 hf8cf82a_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 hfdff14a_1 conda-forge
dill 0.3.4 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gast 0.2.2 py_0 conda-forge
gatkpythonpackages 0.1 pypi_0 pypi
gcc_impl_linux-64 7.5.0 habd7529_20 conda-forge
gcc_linux-64 7.5.0 h47867f9_33 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
gfortran_impl_linux-64 7.5.0 h56cb351_20 conda-forge
gfortran_linux-64 7.5.0 h78c8a43_33 conda-forge
glib 2.66.3 h58526e2_0 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
grpcio 1.38.1 py36h8e87921_0 conda-forge
gsl 2.6 he838d99_2 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
gxx_impl_linux-64 7.5.0 hd0bb8aa_20 conda-forge
gxx_linux-64 7.5.0 h555fc39_33 conda-forge
h5py 2.10.0 nompi_py36h4510012_106 conda-forge
harfbuzz 2.4.0 h9f30f68_3 conda-forge
hdf5 1.10.6 nompi_h3c11f04_101 conda-forge
icu 64.2 he1b5a44_1 conda-forge
importlib-metadata 4.8.1 py36h5fab9bb_0 conda-forge
intel-openmp 2019.4 243
joblib 1.1.1 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
keras 2.2.4 py36_1 conda-forge
keras-applications 1.0.8 py_1 conda-forge
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge
kiwisolver 1.3.1 py36h605e78d_1 conda-forge
krb5 1.16.4 h2fd8d38_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libclang 9.0.1 default_hb4e5071_5 conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-devel_linux-64 7.5.0 hda03d7c_20 conda-forge
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
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libgfortran 3.0.0 1 conda-forge
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libglib 2.66.3 hbe7bbb4_0 conda-forge
libgomp 14.1.0 h77fa898_0 conda-forge
libgpuarray 0.7.6 h7f98852_1003 conda-forge
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libllvm9 9.0.1 default_hc23dcda_7 conda-forge
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libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 7.5.0 hb016644_20 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge
libtiff 4.2.0 hf544144_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
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libxcb 1.16 hd590300_0 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
llvm-openmp 18.1.7 ha31de31_0 conda-forge
make 4.3 hd18ef5c_1 conda-forge
mako 1.3.5 pyhd8ed1ab_0 conda-forge
markdown 3.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.0.1 py36h8f6f2f9_0 conda-forge
matplotlib 3.2.1 0 conda-forge
matplotlib-base 3.2.1 py36hb8e4980_0 conda-forge
mkl 2019.5 281 conda-forge
mkl-service 2.3.0 py36h516909a_0 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
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nss 3.100 hca3bf56_0 conda-forge
numpy 1.17.5 py36h2aa4a07_1 conda-forge
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openssl 1.1.1w hd590300_0 conda-forge
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
pandas 1.0.3 py36h830a2c2_1 conda-forge
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pip 21.3.1 pyhd8ed1ab_0 conda-forge
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pyqt 5.12.3 py36haa643ae_3 conda-forge
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pyqtwebengine 5.12.1 pypi_0 pypi
pysam 0.15.3 py36hbcae180_3 bioconda
python 3.6.10 h8356626_1011_cpython conda-forge
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python_abi 3.6 2_cp36m conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
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r-munsell 0.5.0 r36h6115d3f_1003 conda-forge
r-nlme 3.1_150 r36h31ca83e_0 conda-forge
r-optparse 1.6.4 r36h6115d3f_0 conda-forge
r-pillar 1.6.1 r36hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r36h6115d3f_1 conda-forge
r-pkgload 1.2.1 r36h03ef668_0 conda-forge
r-plogr 0.2.0 r36h6115d3f_1003 conda-forge
r-praise 1.0.0 r36h6115d3f_1004 conda-forge
r-processx 3.5.2 r36hcfec24a_0 conda-forge
r-ps 1.6.0 r36hcfec24a_0 conda-forge
r-purrr 0.3.4 r36hcfec24a_1 conda-forge
r-r6 2.5.0 r36hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r36h6115d3f_1003 conda-forge
r-rcpp 1.0.6 r36h03ef668_0 conda-forge
r-rematch2 2.1.2 r36h6115d3f_1 conda-forge
r-rlang 0.4.11 r36hcfec24a_0 conda-forge
r-rprojroot 2.0.2 r36hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r36hc72bb7e_0 conda-forge
r-scales 1.1.1 r36h6115d3f_0 conda-forge
r-testthat 3.0.2 r36h03ef668_0 conda-forge
r-tibble 3.1.2 r36hcfec24a_0 conda-forge
r-tidyselect 1.1.1 r36hc72bb7e_0 conda-forge
r-utf8 1.2.1 r36hcfec24a_0 conda-forge
r-vctrs 0.3.8 r36hcfec24a_1 conda-forge
r-viridislite 0.4.0 r36hc72bb7e_0 conda-forge
r-waldo 0.2.5 r36hc72bb7e_0 conda-forge
r-withr 2.4.2 r36hc72bb7e_0 conda-forge
readline 8.2 h8228510_1 conda-forge
scikit-learn 0.23.1 py36h0e1014b_0 conda-forge
scipy 1.0.0 py36_blas_openblas_201 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 58.0.4 py36h5fab9bb_2 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.46.0 h6d4b2fc_0 conda-forge
sysroot_linux-64 2.12 he073ed8_17 conda-forge
tensorboard 1.15.0 py36_0 conda-forge
tensorflow 1.15.0 mkl_py36h4920b83_0
tensorflow-base 1.15.0 mkl_py36he1670d9_0
tensorflow-estimator 1.15.1 pyh2649769_0
termcolor 1.1.0 pyhd8ed1ab_3 conda-forge
theano 1.0.4 py36h831f99a_1002 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h8bc8fbc_6 conda-forge
tornado 6.1 py36h8f6f2f9_1 conda-forge
tqdm 4.65.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
werkzeug 0.16.1 py_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.13.1 py36h8f6f2f9_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 hb711507_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zipp 3.6.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forgeIf it is not possible to get a clean gatk environment inside the compute environment this way then we recommend using our docker image which includes the environment and works just as expected. Please pay attention that version 4.6.1.0 and later requires a more updated conda environment with different library dependencies for GCNV and NVScoreVariants.
I hope this helps.
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This helped. Thank you.
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