[2023-06-17 03:14:47,039] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:14:47,044] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:14:47,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg85fe14aa-4fbd-4e92-ade7-66eddac92ef6/dqc_reference
[2023-06-17 03:14:49,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:14:49,411] [INFO] Task started: Prodigal
[2023-06-17 03:14:49,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg451a7ef6-0be7-451a-852d-7aab14e8b9b1/GCA_028715545.1_ASM2871554v1_genomic.fna.gz | prodigal -d GCA_028715545.1_ASM2871554v1_genomic.fna/cds.fna -a GCA_028715545.1_ASM2871554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:14:52,132] [INFO] Task succeeded: Prodigal
[2023-06-17 03:14:52,133] [INFO] Task started: HMMsearch
[2023-06-17 03:14:52,133] [INFO] Running command: hmmsearch --tblout GCA_028715545.1_ASM2871554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85fe14aa-4fbd-4e92-ade7-66eddac92ef6/dqc_reference/reference_markers.hmm GCA_028715545.1_ASM2871554v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:14:52,338] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:14:52,339] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg451a7ef6-0be7-451a-852d-7aab14e8b9b1/GCA_028715545.1_ASM2871554v1_genomic.fna.gz]
[2023-06-17 03:14:52,377] [INFO] Query marker FASTA was written to GCA_028715545.1_ASM2871554v1_genomic.fna/markers.fasta
[2023-06-17 03:14:52,378] [INFO] Task started: Blastn
[2023-06-17 03:14:52,378] [INFO] Running command: blastn -query GCA_028715545.1_ASM2871554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85fe14aa-4fbd-4e92-ade7-66eddac92ef6/dqc_reference/reference_markers.fasta -out GCA_028715545.1_ASM2871554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:14:53,382] [INFO] Task succeeded: Blastn
[2023-06-17 03:14:53,387] [INFO] Selected 1 target genomes.
[2023-06-17 03:14:53,388] [INFO] Target genome list was writen to GCA_028715545.1_ASM2871554v1_genomic.fna/target_genomes.txt
[2023-06-17 03:14:53,390] [INFO] Task started: fastANI
[2023-06-17 03:14:53,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg451a7ef6-0be7-451a-852d-7aab14e8b9b1/GCA_028715545.1_ASM2871554v1_genomic.fna.gz --refList GCA_028715545.1_ASM2871554v1_genomic.fna/target_genomes.txt --output GCA_028715545.1_ASM2871554v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:14:53,917] [INFO] Task succeeded: fastANI
[2023-06-17 03:14:53,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85fe14aa-4fbd-4e92-ade7-66eddac92ef6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:14:53,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85fe14aa-4fbd-4e92-ade7-66eddac92ef6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:14:53,919] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:14:53,919] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 03:14:53,919] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-17 03:14:53,922] [INFO] DFAST Taxonomy check result was written to GCA_028715545.1_ASM2871554v1_genomic.fna/tc_result.tsv
[2023-06-17 03:14:53,923] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:14:53,923] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:14:53,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85fe14aa-4fbd-4e92-ade7-66eddac92ef6/dqc_reference/checkm_data
[2023-06-17 03:14:53,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:14:53,947] [INFO] Task started: CheckM
[2023-06-17 03:14:53,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028715545.1_ASM2871554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028715545.1_ASM2871554v1_genomic.fna/checkm_input GCA_028715545.1_ASM2871554v1_genomic.fna/checkm_result
[2023-06-17 03:15:10,493] [INFO] Task succeeded: CheckM
[2023-06-17 03:15:10,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:15:10,515] [INFO] ===== Completeness check finished =====
[2023-06-17 03:15:10,515] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:15:10,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028715545.1_ASM2871554v1_genomic.fna/markers.fasta)
[2023-06-17 03:15:10,516] [INFO] Task started: Blastn
[2023-06-17 03:15:10,516] [INFO] Running command: blastn -query GCA_028715545.1_ASM2871554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85fe14aa-4fbd-4e92-ade7-66eddac92ef6/dqc_reference/reference_markers_gtdb.fasta -out GCA_028715545.1_ASM2871554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:15:10,956] [INFO] Task succeeded: Blastn
[2023-06-17 03:15:10,960] [INFO] Selected 7 target genomes.
[2023-06-17 03:15:10,960] [INFO] Target genome list was writen to GCA_028715545.1_ASM2871554v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:15:10,971] [INFO] Task started: fastANI
[2023-06-17 03:15:10,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg451a7ef6-0be7-451a-852d-7aab14e8b9b1/GCA_028715545.1_ASM2871554v1_genomic.fna.gz --refList GCA_028715545.1_ASM2871554v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028715545.1_ASM2871554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:15:13,131] [INFO] Task succeeded: fastANI
[2023-06-17 03:15:13,138] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 03:15:13,138] [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_002495885.1	s__UBA148 sp002495885	92.3806	317	371	d__Archaea;p__Halobacteriota;c__UBA148;o__UBA148;f__UBA148;g__UBA148	95.0	99.74	99.74	0.80	0.80	2	-
GCA_013415795.1	s__UBA148 sp013415795	82.9551	207	371	d__Archaea;p__Halobacteriota;c__UBA148;o__UBA148;f__UBA148;g__UBA148	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:15:13,141] [INFO] GTDB search result was written to GCA_028715545.1_ASM2871554v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:15:13,142] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:15:13,145] [INFO] DFAST_QC result json was written to GCA_028715545.1_ASM2871554v1_genomic.fna/dqc_result.json
[2023-06-17 03:15:13,145] [INFO] DFAST_QC completed!
[2023-06-17 03:15:13,146] [INFO] Total running time: 0h0m26s