[2024-01-24 13:49:30,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgd350761a-d853-48f9-969b-be334612786b/dqc_reference
[2024-01-24 13:49:32,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,014] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg815f3a85-f313-430c-9f5a-830bce66ef5a/GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/cds.fna -a GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:47,046] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:47,046] [INFO] Task started: HMMsearch
[2024-01-24 13:49:47,046] [INFO] Running command: hmmsearch --tblout GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd350761a-d853-48f9-969b-be334612786b/dqc_reference/reference_markers.hmm GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:47,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:47,400] [INFO] Found 6/6 markers.
[2024-01-24 13:49:47,445] [INFO] Query marker FASTA was written to GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:47,445] [INFO] Task started: Blastn
[2024-01-24 13:49:47,445] [INFO] Running command: blastn -query GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd350761a-d853-48f9-969b-be334612786b/dqc_reference/reference_markers.fasta -out GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,715] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:48,716] [INFO] Target genome list was writen to GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:48,723] [INFO] Task started: fastANI
[2024-01-24 13:49:48,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg815f3a85-f313-430c-9f5a-830bce66ef5a/GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna.gz --refList GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:05,433] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:05,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd350761a-d853-48f9-969b-be334612786b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:05,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd350761a-d853-48f9-969b-be334612786b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:05,447] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:05,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:05,448] [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
Williamsia sterculiae	strain=CPCC 203464	GCA_900156495.1	1344003	1344003	type	True	100.0	1467	1470	95	conclusive
Williamsia phyllosphaerae	strain=CCM 7855	GCA_014635305.1	885042	885042	type	True	78.8863	586	1470	95	below_threshold
Williamsia maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	78.8635	611	1470	95	below_threshold
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	78.8447	591	1470	95	below_threshold
Williamsia serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	78.7744	559	1470	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	78.618	538	1470	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	78.6107	546	1470	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	78.5211	480	1470	95	below_threshold
Williamsia deligens	strain=DSM 44902	GCA_024171765.1	321325	321325	type	True	78.4993	559	1470	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	78.4807	517	1470	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	78.3845	524	1470	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	78.2527	423	1470	95	below_threshold
Gordonia sputi	strain=ATCC 29627	GCA_012396255.1	36823	36823	type	True	78.2165	407	1470	95	below_threshold
Gordonia sputi	strain=NBRC 100414	GCA_000248055.2	36823	36823	type	True	78.1667	407	1470	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	77.7709	386	1470	95	below_threshold
Nocardia stercoris	strain=NEAU-LL90	GCA_003696265.1	2483361	2483361	type	True	77.187	378	1470	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	76.073	239	1470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:05,450] [INFO] DFAST Taxonomy check result was written to GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:05,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:05,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:05,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd350761a-d853-48f9-969b-be334612786b/dqc_reference/checkm_data
[2024-01-24 13:50:05,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:05,494] [INFO] Task started: CheckM
[2024-01-24 13:50:05,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/checkm_input GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:51:01,093] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:01,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:01,118] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:01,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:01,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:51:01,119] [INFO] Task started: Blastn
[2024-01-24 13:51:01,119] [INFO] Running command: blastn -query GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd350761a-d853-48f9-969b-be334612786b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:02,739] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:02,743] [INFO] Selected 20 target genomes.
[2024-01-24 13:51:02,743] [INFO] Target genome list was writen to GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:02,773] [INFO] Task started: fastANI
[2024-01-24 13:51:02,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg815f3a85-f313-430c-9f5a-830bce66ef5a/GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna.gz --refList GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:21,438] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:21,465] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:21,465] [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_900156495.1	s__Williamsia_B sterculiae	100.0	1467	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014635305.1	s__Williamsia_A phyllosphaerae	78.8641	589	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964005.1	s__Williamsia_A herbipolensis	78.8307	593	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	95.03	95.03	0.89	0.89	2	-
GCA_016462415.1	s__Williamsia_A sp016462415	78.8092	548	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327325.1	s__Gordonia rubripertincta	78.6486	474	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_001485495.1	s__Gordonia desulfuricans	78.6139	538	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_018474015.1	s__Williamsia_A sp018474015	78.5378	477	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298235.1	s__Gordonia namibiensis	78.5341	490	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000225505.1	s__Gordonia alkanivorans	78.5294	479	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_900105725.1	s__Gordonia westfalica	78.5036	514	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855095.1	s__Gordonia insulae	78.384	524	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348785.1	s__Gordonia sp013348785	78.2628	401	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014673215.1	s__Gordonia hankookensis	78.2385	469	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	-
GCF_009914535.1	s__Gordonia pseudoamarae	78.1766	419	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.95	99.95	1.00	1.00	2	-
GCF_000248055.1	s__Gordonia sputi	78.1478	409	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.92	96.52	0.90	0.84	5	-
GCF_000192435.1	s__Gordonia neofelifaecis	78.0349	366	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108565.1	s__Mycobacterium rutilum	77.5121	369	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696265.1	s__Nocardia stercoris	77.2261	372	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	76.5497	293	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716595.1	s__Actinosynnema sp000716595	76.2744	278	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:21,467] [INFO] GTDB search result was written to GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:21,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:21,471] [INFO] DFAST_QC result json was written to GCF_900156495.1_IMG-taxon_2681812929_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:51:21,472] [INFO] DFAST_QC completed!
[2024-01-24 13:51:21,472] [INFO] Total running time: 0h1m51s