[2023-06-13 04:36:02,884] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:36:02,887] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:36:02,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e3e0e27-37a1-4a09-b49c-c16b6c9377c0/dqc_reference
[2023-06-13 04:36:04,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:36:04,177] [INFO] Task started: Prodigal
[2023-06-13 04:36:04,177] [INFO] Running command: gunzip -c /var/lib/cwl/stga6b2d222-5222-4230-9afe-05b1bf8e73fe/GCA_022866945.1_ASM2286694v1_genomic.fna.gz | prodigal -d GCA_022866945.1_ASM2286694v1_genomic.fna/cds.fna -a GCA_022866945.1_ASM2286694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:36:07,046] [INFO] Task succeeded: Prodigal
[2023-06-13 04:36:07,047] [INFO] Task started: HMMsearch
[2023-06-13 04:36:07,047] [INFO] Running command: hmmsearch --tblout GCA_022866945.1_ASM2286694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e3e0e27-37a1-4a09-b49c-c16b6c9377c0/dqc_reference/reference_markers.hmm GCA_022866945.1_ASM2286694v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:36:07,246] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:36:07,247] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga6b2d222-5222-4230-9afe-05b1bf8e73fe/GCA_022866945.1_ASM2286694v1_genomic.fna.gz]
[2023-06-13 04:36:07,266] [INFO] Query marker FASTA was written to GCA_022866945.1_ASM2286694v1_genomic.fna/markers.fasta
[2023-06-13 04:36:07,266] [INFO] Task started: Blastn
[2023-06-13 04:36:07,267] [INFO] Running command: blastn -query GCA_022866945.1_ASM2286694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e3e0e27-37a1-4a09-b49c-c16b6c9377c0/dqc_reference/reference_markers.fasta -out GCA_022866945.1_ASM2286694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:07,751] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:07,756] [INFO] Selected 0 target genomes.
[2023-06-13 04:36:07,757] [INFO] Target genome list was writen to GCA_022866945.1_ASM2286694v1_genomic.fna/target_genomes.txt
[2023-06-13 04:36:07,757] [ERROR] File is empty. [GCA_022866945.1_ASM2286694v1_genomic.fna/target_genomes.txt]
[2023-06-13 04:36:07,757] [ERROR] Task failed. No target genome found.
[2023-06-13 04:36:07,757] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:36:07,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e3e0e27-37a1-4a09-b49c-c16b6c9377c0/dqc_reference/checkm_data
[2023-06-13 04:36:07,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:36:07,782] [INFO] Task started: CheckM
[2023-06-13 04:36:07,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022866945.1_ASM2286694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022866945.1_ASM2286694v1_genomic.fna/checkm_input GCA_022866945.1_ASM2286694v1_genomic.fna/checkm_result
[2023-06-13 04:36:24,878] [INFO] Task succeeded: CheckM
[2023-06-13 04:36:24,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.82%
Contamintation: 8.68%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:36:24,916] [INFO] ===== Completeness check finished =====
[2023-06-13 04:36:24,916] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:36:24,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022866945.1_ASM2286694v1_genomic.fna/markers.fasta)
[2023-06-13 04:36:24,917] [INFO] Task started: Blastn
[2023-06-13 04:36:24,917] [INFO] Running command: blastn -query GCA_022866945.1_ASM2286694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e3e0e27-37a1-4a09-b49c-c16b6c9377c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022866945.1_ASM2286694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:25,383] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:25,387] [INFO] Selected 2 target genomes.
[2023-06-13 04:36:25,387] [INFO] Target genome list was writen to GCA_022866945.1_ASM2286694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:36:25,390] [INFO] Task started: fastANI
[2023-06-13 04:36:25,390] [INFO] Running command: fastANI --query /var/lib/cwl/stga6b2d222-5222-4230-9afe-05b1bf8e73fe/GCA_022866945.1_ASM2286694v1_genomic.fna.gz --refList GCA_022866945.1_ASM2286694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022866945.1_ASM2286694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:36:26,111] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:26,124] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 04:36:26,124] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_004376385.1	s__BIN-L-1 sp004376385	82.7912	146	237	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__BA1;g__BIN-L-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003096235.1	s__BIN-L-1 sp003096235	79.5144	154	237	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__BA1;g__BIN-L-1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:36:26,127] [INFO] GTDB search result was written to GCA_022866945.1_ASM2286694v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:36:26,128] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:36:26,131] [INFO] DFAST_QC result json was written to GCA_022866945.1_ASM2286694v1_genomic.fna/dqc_result.json
[2023-06-13 04:36:26,131] [INFO] DFAST_QC completed!
[2023-06-13 04:36:26,131] [INFO] Total running time: 0h0m23s