[2024-01-25 17:35:50,429] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:50,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:50,430] [INFO] DQC Reference Directory: /var/lib/cwl/stgac12e434-9254-4584-a04b-12c5f07ce726/dqc_reference
[2024-01-25 17:35:51,542] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:51,543] [INFO] Task started: Prodigal
[2024-01-25 17:35:51,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg87d7ca98-9f62-44f1-b36b-0995621001b5/GCF_003797185.1_ASM379718v1_genomic.fna.gz | prodigal -d GCF_003797185.1_ASM379718v1_genomic.fna/cds.fna -a GCF_003797185.1_ASM379718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:12,529] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:12,529] [INFO] Task started: HMMsearch
[2024-01-25 17:36:12,529] [INFO] Running command: hmmsearch --tblout GCF_003797185.1_ASM379718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac12e434-9254-4584-a04b-12c5f07ce726/dqc_reference/reference_markers.hmm GCF_003797185.1_ASM379718v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:12,776] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:12,777] [INFO] Found 6/6 markers.
[2024-01-25 17:36:12,814] [INFO] Query marker FASTA was written to GCF_003797185.1_ASM379718v1_genomic.fna/markers.fasta
[2024-01-25 17:36:12,815] [INFO] Task started: Blastn
[2024-01-25 17:36:12,815] [INFO] Running command: blastn -query GCF_003797185.1_ASM379718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac12e434-9254-4584-a04b-12c5f07ce726/dqc_reference/reference_markers.fasta -out GCF_003797185.1_ASM379718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:13,989] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:13,991] [INFO] Selected 9 target genomes.
[2024-01-25 17:36:13,992] [INFO] Target genome list was writen to GCF_003797185.1_ASM379718v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:13,997] [INFO] Task started: fastANI
[2024-01-25 17:36:13,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg87d7ca98-9f62-44f1-b36b-0995621001b5/GCF_003797185.1_ASM379718v1_genomic.fna.gz --refList GCF_003797185.1_ASM379718v1_genomic.fna/target_genomes.txt --output GCF_003797185.1_ASM379718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:23,966] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:23,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac12e434-9254-4584-a04b-12c5f07ce726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:23,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac12e434-9254-4584-a04b-12c5f07ce726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:23,974] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:23,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:23,974] [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
Gordonia oryzae	strain=RS15-1S	GCA_003797185.1	2487349	2487349	type	True	100.0	1492	1492	95	conclusive
Gordonia polyisoprenivorans	strain=ATCC BAA-14	GCA_012396285.1	84595	84595	type	True	92.7123	1322	1492	95	below_threshold
Gordonia polyisoprenivorans	strain=NBRC 16320	GCA_000241325.2	84595	84595	type	True	92.6759	1310	1492	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	80.5604	847	1492	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	80.4854	889	1492	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	79.6242	736	1492	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	79.5604	755	1492	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.4622	669	1492	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	79.3659	677	1492	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:23,975] [INFO] DFAST Taxonomy check result was written to GCF_003797185.1_ASM379718v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:23,976] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:23,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:23,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac12e434-9254-4584-a04b-12c5f07ce726/dqc_reference/checkm_data
[2024-01-25 17:36:23,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:24,020] [INFO] Task started: CheckM
[2024-01-25 17:36:24,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003797185.1_ASM379718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003797185.1_ASM379718v1_genomic.fna/checkm_input GCF_003797185.1_ASM379718v1_genomic.fna/checkm_result
[2024-01-25 17:37:27,390] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:27,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:27,410] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:27,411] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:27,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003797185.1_ASM379718v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:27,412] [INFO] Task started: Blastn
[2024-01-25 17:37:27,412] [INFO] Running command: blastn -query GCF_003797185.1_ASM379718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac12e434-9254-4584-a04b-12c5f07ce726/dqc_reference/reference_markers_gtdb.fasta -out GCF_003797185.1_ASM379718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:29,051] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:29,054] [INFO] Selected 9 target genomes.
[2024-01-25 17:37:29,054] [INFO] Target genome list was writen to GCF_003797185.1_ASM379718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:29,060] [INFO] Task started: fastANI
[2024-01-25 17:37:29,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg87d7ca98-9f62-44f1-b36b-0995621001b5/GCF_003797185.1_ASM379718v1_genomic.fna.gz --refList GCF_003797185.1_ASM379718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003797185.1_ASM379718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:40,960] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:40,966] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:40,967] [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
GCF_003797185.1	s__Gordonia oryzae	100.0	1492	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000241325.1	s__Gordonia polyisoprenivorans	92.6685	1312	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.60	97.62	0.90	0.79	11	-
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	91.7758	1313	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485495.1	s__Gordonia desulfuricans	80.5906	842	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_000024785.1	s__Gordonia bronchialis	79.6523	729	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900105725.1	s__Gordonia westfalica	79.5436	717	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298235.1	s__Gordonia namibiensis	79.4949	664	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCA_004193205.1	s__Gordonia sediminis	79.3302	708	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	75.8379	209	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:40,968] [INFO] GTDB search result was written to GCF_003797185.1_ASM379718v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:40,969] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:40,974] [INFO] DFAST_QC result json was written to GCF_003797185.1_ASM379718v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:40,974] [INFO] DFAST_QC completed!
[2024-01-25 17:37:40,974] [INFO] Total running time: 0h1m51s