Building DAG of jobs... Using shell: /bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Provided resources: mem_mb=64000 Conda environments: ignored Job counts: count jobs 1 LongOrfs 1 Predict 1 all 24 assemble_transcripts_fq 1 base_recalibration 1 blastp 1 call_gvcf_varaints 1 call_vcf_variants 1 cdna_alignment_orf_to_genome_orf 1 copy_gff3_to_snpeff 1 custom_protein_xml 1 dict_fa 1 download_dbsnp_vcf 1 download_ensembl_references 1 download_protein_xml 1 final_vcf_naming 1 finish_isoform 1 finish_isoform_variants 1 finish_variants 1 generate_reference_snpeff_database 1 generate_snpeff_database 1 gtf_file_to_cDNA_seqs 1 gtf_to_alignment_gff3 24 hisat2_align_bam_fq 1 hisat2_groupmark_bam 1 hisat2_merge_bams 1 hisat2_splice_sites 1 hisat_genome 1 index_ensembl_vcf 1 index_fa 1 makeblastdb 1 merge_transcripts 1 reference_protein_xml 1 remove_exon_and_utr_information 1 reorder_genome_fasta 1 split_n_cigar_reads 1 transfer_modifications_isoformvariant 1 transfer_modifications_variant 1 variant_annotation_custom 1 variant_annotation_ref 86 [Mon Mar 29 13:56:51 2021] rule download_protein_xml: output: data/uniprot/Homo_sapiens.protein.xml.gz, data/uniprot/Homo_sapiens.protein.fasta log: data/uniprot/Homo_sapiens.protein.xml.gz.log jobid: 73 benchmark: data/uniprot/Homo_sapiens.protein.xml.gz.benchmark [Mon Mar 29 13:56:51 2021] rule download_ensembl_references: output: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.fa, data/ensembl/Homo_sapiens.GRCh38.97.gff3, data/ensembl/Homo_sapiens.GRCh38.pep.all.fa log: data/ensembl/downloads.log jobid: 6 benchmark: data/ensembl/downloads.benchmark [Mon Mar 29 13:56:51 2021] rule download_dbsnp_vcf: input: ChromosomeMappings/GRCh38_UCSC2ensembl.txt output: data/ensembl/Homo_sapiens.ensembl.vcf log: data/ensembl/downloads_dbsnp_vcf.log jobid: 11 benchmark: data/ensembl/downloads_dbsnp_vcf.benchmark [Mon Mar 29 14:01:58 2021] Finished job 73. 1 of 86 steps (1%) done [Mon Mar 29 14:01:58 2021] rule makeblastdb: input: data/uniprot/Homo_sapiens.protein.fasta output: data/uniprot/Homo_sapiens.protein.fasta.pin, data/uniprot/Homo_sapiens.protein.fasta.phr, data/uniprot/Homo_sapiens.protein.fasta.psq log: data/uniprot/Homo_sapiens.proteinmakeblastdb.log jobid: 110 benchmark: data/uniprot/Homo_sapiens.proteinmakeblastdb.benchmark [Mon Mar 29 14:02:01 2021] Finished job 110. 2 of 86 steps (2%) done [Mon Mar 29 14:04:16 2021] Finished job 11. 3 of 86 steps (3%) done [Mon Mar 29 14:04:16 2021] rule index_ensembl_vcf: input: data/ensembl/Homo_sapiens.ensembl.vcf output: data/ensembl/Homo_sapiens.ensembl.vcf.idx log: data/ensembl/Homo_sapiens.ensembl.vcf.idx.log jobid: 13 [Mon Mar 29 14:07:11 2021] Finished job 13. 4 of 86 steps (5%) done [Mon Mar 29 14:08:21 2021] Finished job 6. 5 of 86 steps (6%) done [Mon Mar 29 14:08:21 2021] rule hisat2_splice_sites: input: data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt log: data/ensembl/Homo_sapiens.GRCh38.97.splicesites.log jobid: 21 [Mon Mar 29 14:08:21 2021] rule reorder_genome_fasta: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.fa output: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa log: data/ensembl/karyotypic_order.log jobid: 7 benchmark: data/ensembl/karyotypic_order.benchmark [Mon Mar 29 14:08:27 2021] Finished job 21. 6 of 86 steps (7%) done [Mon Mar 29 14:09:02 2021] Finished job 7. 7 of 86 steps (8%) done [Mon Mar 29 14:09:02 2021] rule hisat_genome: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, data/ensembl/done_building_hisat_genomeHomo_sapiens.GRCh38.txt log: data/ensembl/Homo_sapiens.GRCh38.hisatbuild.log jobid: 19 benchmark: data/ensembl/Homo_sapiens.GRCh38.hisatbuild.benchmark threads: 12 [Mon Mar 29 14:09:02 2021] rule dict_fa: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa output: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.dict log: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.dict.log jobid: 70 [Mon Mar 29 14:09:02 2021] rule index_fa: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa output: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa.fai log: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa.log jobid: 69 [Mon Mar 29 14:09:02 2021] rule generate_reference_snpeff_database: input: SnpEff/snpEff.jar, data/ensembl/Homo_sapiens.GRCh38.97.gff3, data/ensembl/Homo_sapiens.GRCh38.pep.all.fa, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa output: SnpEff/data/Homo_sapiens.GRCh38/protein.fa, SnpEff/data/Homo_sapiens.GRCh38/genes.gff, SnpEff/data/genomes/Homo_sapiens.GRCh38.fa, SnpEff/data/Homo_sapiens.GRCh38/doneHomo_sapiens.GRCh38.txt log: SnpEff/data/Homo_sapiens.GRCh38/snpeffdatabase.log jobid: 4 benchmark: SnpEff/data/Homo_sapiens.GRCh38/snpeffdatabase.benchmark resources: mem_mb=16000 [Mon Mar 29 14:09:23 2021] Finished job 70. 8 of 86 steps (9%) done [Mon Mar 29 14:09:28 2021] Finished job 69. 9 of 86 steps (10%) done [Mon Mar 29 14:12:15 2021] Finished job 4. 10 of 86 steps (12%) done ProtectedOutputException in line 89 of /home/animeshs/Spritz/Spritz/rules/proteogenomics.smk: Write-protected output files for rule reference_protein_xml: /home/animeshs/rnAGS/variants/doneHomo_sapiens.GRCh38.97.txt /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml.gz /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.fasta /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withdecoys.fasta /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withmods.xml.gz File "/home/animeshs/miniconda3/envs/spritz/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 131, in run_jobs File "/home/animeshs/miniconda3/envs/spritz/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 433, in run File "/home/animeshs/miniconda3/envs/spritz/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 225, in _run File "/home/animeshs/miniconda3/envs/spritz/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 150, in _run