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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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`pVACseq ` terminated with an error exit status (1) #66

Closed sasi-arunachalam closed 2 months ago

sasi-arunachalam commented 7 months ago

Dear author, Thank you for the nice pipeline. I recently ran nextNEOpi pipeline on one sample( DNA tumor, DNA normal and RNA tumor). The pipeline produced all expected five folders. However, in analysis folder 4 subfolders (pVACseq,mixMHC2pred,CSIN,IGS,BCR_TCR)) were missing.

A)I have attached the screen shot of overall run Screenshot 2023-11-27 at 7 31 56 PM

B) I believe the error is ValueError: Input X contains NaN.

Below is the copy paste of actual error

Error executing process > 'pVACseq (10-TM-FreshFrozen)'

Caused by: Process pVACseq (10-TM-FreshFrozen) terminated with an error exit status (1)

Command executed:

pvacseq run \ --iedb-install-directory /opt/iedb \ -t 10 \ -p 10-TM-FreshFrozen_vep_phased.vcf.gz \ -e1 8,9,10,11 \ -e2 15,16,17,18,19,20,21,22,23,24,25 \ --normal-sample-name 10-TM-FreshFrozen_normal \ --tumor-purity 1 \ \ --netmhc-stab \ --binding-threshold 500 --top-score-metric median --minimum-fold-change 0.0 --normal-cov 5 --tdna-cov 10 --trna-cov 10 --normal-vaf 0.02 --tdna-vaf 0.25 --trna-vaf 0.25 --expn-val 1 --maximum-transcript-support-level 1 \ 10-TM-FreshFrozen_vep_somatic_gx.vcf.gz 10-TM-FreshFrozen_tumor HLA-B*18:01 NetMHCpan NetMHCpanEL MHCflurry MHCflurryEL NetMHCIIpan NetMHCIIpanEL ./

if [ -e ./MHC_Class_I/10-TM-FreshFrozen_tumor.filtered.tsv ]; then mv ./MHC_Class_I/10-TM-FreshFrozen_tumor.filtered.tsv ./MHC_Class_I/10-TM-FreshFrozen_tumor_HLA-B18:01.filtered.tsv fi if [ -e ./MHC_Class_I/10-TM-FreshFrozen_tumor.all_epitopes.tsv ]; then mv ./MHC_Class_I/10-TM-FreshFrozen_tumor.all_epitopes.tsv ./MHC_Class_I/10-TM-FreshFrozen_tumor_HLA-B18:01.all_epitopes.tsv fi if [ -e ./MHC_Class_II/10-TM-FreshFrozen_tumor.filtered.tsv ]; then mv ./MHC_Class_II/10-TM-FreshFrozen_tumor.filtered.tsv ./MHC_Class_II/10-TM-FreshFrozen_tumor_HLA-B18:01.filtered.tsv fi if [ -e ./MHC_Class_II/10-TM-FreshFrozen_tumor.all_epitopes.tsv ]; then mv ./MHC_Class_II/10-TM-FreshFrozen_tumor.all_epitopes.tsv ./MHC_Class_II/10-TM-FreshFrozen_tumor_HLA-B18:01.all_epitopes.tsv fi

Command exit status: 1

Command output: Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.8.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.9.tsv_201-242 Making binding predic10.tsv_201-242 Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.10.tsv_201-242 Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.8.tsv_1-200 Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.11.tsv_201-242 Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.9.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.9.tsv_201-242 Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.8.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.9.tsv_201-242 Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.10.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.11.tsv_201-242 Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.9.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.11.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.11.tsv_201-242 Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.8.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.8.tsv_201-242 Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.10.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.10.tsv_201-242 Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.8.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.8.tsv_1-200 Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.11.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.11.tsv_1-200 Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.10.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.10.tsv_1-200 Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.9.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.9.tsv_1-200 Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.11.tsv_201-242 - Completed Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method MHCflurry - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.9.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.8.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.10.tsv_201-242 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.9.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.9.tsv_1-200 Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.8.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.8.tsv_1-200 Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.10.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.10.tsv_1-200 Making binding predictions on Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.9.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpan - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan.HLA-B18:01.11.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.11.tsv_1-200 Making binding predictions on Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.8.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.10.tsv_1-200 - Completed Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpanEL - File MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.netmhcpan_el.HLA-B18:01.11.tsv_1-200 - Completed

Command error: /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/tensorflow/python/ops/init_ops.py:94: calling VarianceScaling.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/tensorflow/python/ops/init_ops.py:94: calling Zeros.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/tensorflow/python/ops/init_ops.py:94: calling VarianceScaling.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/tensorflow/python/ops/init_ops.py:94: calling Zeros.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, CRITICAL:pymp:An exception occured in thread 8: (<class 'ValueError'>, Input X contains NaN. LogisticRegression does not accept missing values encoded as NaN natively. For supervised learning, you might want to consider sklearn.ensemble.HistGradientBoostingClassifier and Regressor which accept missing values encoded as NaNs natively. Alternatively, it is possible to preprocess the data, for instance by using an imputer transformer in a pipeline or drop samples with missing values. See https://scikit-learn.org/stable/modules/impute.html You can find a list of all estimators that handle NaN values at the following page: https://scikit-learn.org/stable/modules/impute.html#estimators-that-handle-nan-values). Traceback (most recent call last): File "/opt/conda/bin/pvacseq", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/pvactools/tools/pvacseq/main.py", line 123, in main args[0].func.main(args[1]) File "/opt/conda/lib/python3.8/site-packages/pvactools/tools/pvacseq/run.py", line 138, in main pipeline.execute() File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/pipeline.py", line 451, in execute self.call_iedb(chunks) File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/pipeline.py", line 357, in call_iedb p.print("Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s - Completed" % (a, epl, method, filename)) File "/opt/conda/lib/python3.8/site-packages/pymp/init.py", line 148, in exit raise exc_t(exc_val) ValueError: Input X contains NaN. LogisticRegression does not accept missing values encoded as NaN natively. For supervised learning, you might want to consider sklearn.ensemble.HistGradientBoostingClassifier and Regressor which accept missing values encoded as NaNs natively. Alternatively, it is possible to preprocess the data, for instance by using an imputer transformer in a pipeline or drop samples with missing values. See https://scikit-learn.org/stable/modules/impute.html You can find a list of all estimators that handle NaN values at the following page: https://scikit-learn.org/stable/modules/impute.html#estimators-that-handle-nan-values INFO: Cleaning up image...

Work dir: /home/ubuntu/epitope/work_normal/64/dfceaa8042580a81220fa7d392d531

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

sasi-arunachalam commented 7 months ago

(singularity) ubuntu@ip-172-31-6-189:~/epitope/work_normal/64/dfceaa8042580a81220fa7d392d531$ bash .command.run

INFO: Converting SIF file to temporary sandbox... Executing MHC Class I predictions Converting .vcf to TSV TSV file already exists. Skipping. Converting VCF to TSV Warning: Proximal variant is not a missense mutation and will be skipped: chr2 140700416 Warning: Proximal variant is not a missense mutation and will be skipped: chr12 120641069 Warning: Proximal variant is not a missense mutation and will be skipped: chr20 5302730 Completed Generating Variant Peptide FASTA and Key File Completed Parsing the Variant Peptide FASTA and Key File Completed Calculating Manufacturability Metrics Completed Splitting TSV into smaller chunks Splitting TSV into smaller chunks - Entries 1-100 Split TSV file for Entries 1-100 already exists. Skipping. Splitting TSV into smaller chunks - Entries 101-121 Split TSV file for Entries 101-121 already exists. Skipping. Completed Generating Variant Peptide FASTA and Key Files Split FASTA file for Epitope Length 8 - Entries 1-200 already exists. Skipping. Split FASTA file for Epitope Length 9 - Entries 1-200 already exists. Skipping. Split FASTA file for Epitope Length 10 - Entries 1-200 already exists. Skipping. Split FASTA file for Epitope Length 11 - Entries 1-200 already exists. Skipping. Split FASTA file for Epitope Length 8 - Entries 201-242 already exists. Skipping. Split FASTA file for Epitope Length 9 - Entries 201-242 already exists. Skipping. Split FASTA file for Epitope Length 10 - Entries 201-242 already exists. Skipping. Split FASTA file for Epitope Length 11 - Entries 201-242 already exists. Skipping. Completed Prediction file for Allele HLA-B18:01 and Epitope Length 8 with Method MHCflurry (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpan (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpanEL (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 9 with Method MHCflurry (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpan (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpanEL (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 10 with Method MHCflurry (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpan (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpanEL (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 11 with Method MHCflurry (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpan (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpanEL (Entries 1-200) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 8 with Method MHCflurry (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpan (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 8 with Method NetMHCpanEL (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 9 with Method MHCflurry (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpan (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 9 with Method NetMHCpanEL (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 10 with Method MHCflurry (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpan (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 10 with Method NetMHCpanEL (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpan (Entries 201-242) already exists. Skipping. Prediction file for Allele HLA-B18:01 and Epitope Length 11 with Method NetMHCpanEL (Entries 201-242) already exists. Skipping. Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method MHCflurry - File /home/ubuntu/epitope/work_normal/64/dfceaa8042580a81220fa7d392d531/MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.11.tsv_201-242 WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/keras/src/initializers/initializers_v1.py:297: calling RandomUniform.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/tensorflow/python/ops/init_ops.py:94: calling VarianceScaling.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor WARNING:tensorflow:From /opt/conda/lib/python3.8/site-packages/tensorflow/python/ops/init_ops.py:94: calling Zeros.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor Forcing tensorflow backend. Making binding predictions on Allele HLA-B18:01 and Epitope Length 11 with Method MHCflurry - File /home/ubuntu/epitope/work_normal/64/dfceaa8042580a81220fa7d392d531/MHC_Class_I/tmp/10-TM-FreshFrozen_tumor.MHCflurry.HLA-B18:01.11.tsv_201-242 - Completed /opt/conda/lib/python3.8/site-packages/keras/src/engine/training_v1.py:2359: UserWarning: Model.state_updates will be removed in a future version. This property should not be used in TensorFlow 2.0, as updates are applied automatically. updates=self.state_updates, Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 8 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 8 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 8 - Entries 1-200 - Completed Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 9 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 9 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 9 - Entries 1-200 - Completed Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 10 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 10 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 10 - Entries 1-200 - Completed Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 11 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 11 - Entries 1-200 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 11 - Entries 1-200 - Completed Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 8 - Entries 201-242 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 8 - Entries 201-242 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 8 - Entries 201-242 - Completed Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 9 - Entries 201-242 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 9 - Entries 201-242 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 9 - Entries 201-242 - Completed Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 10 - Entries 201-242 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 10 - Entries 201-242 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 10 - Entries 201-242 - Completed Parsing binding predictions for Allele HLA-B18:01 and Epitope Length 11 - Entries 201-242 Parsing prediction file for Allele HLA-B18:01 and Epitope Length 11 - Entries 201-242 Parsing prediction file for Allele HLA-B*18:01 and Epitope Length 11 - Entries 201-242 - Completed Combining Parsed Prediction Files Completed Creating aggregated report Tumor clonal VAF estimated as 0.5 (calculated from user-provided tumor purity of 1.0). Assuming variants with VAF < 0.25 are subclonal Completed Calculating Manufacturability Metrics Completed Running Binding Filters Completed Running Coverage Filters Completed Running Transcript Support Level Filter Complete Running Top Score Filter Completed Running NetMHCStabPan Completed

Done: Pipeline finished successfully. File /home/ubuntu/epitope/work_normal/64/dfceaa8042580a81220fa7d392d531/MHC_Class_I/10-TM-FreshFrozen_tumor.filtered.tsv contains list of filtered putative neoantigens.

No MHC class II alleles chosen. Skipping MHC class II predictions. INFO: Cleaning up image...

riederd commented 2 months ago

Should be fixed now in v1.4.1, please reopen if not.