[2024-01-25 18:54:20,407] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:20,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:20,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg02e0bbc9-7e38-4d51-9552-b2ad45a65f0f/dqc_reference
[2024-01-25 18:54:21,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:21,573] [INFO] Task started: Prodigal
[2024-01-25 18:54:21,573] [INFO] Running command: gunzip -c /var/lib/cwl/stgee08a70f-382b-46d5-92eb-8d73e4d08b25/GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/cds.fna -a GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:39,769] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:39,770] [INFO] Task started: HMMsearch
[2024-01-25 18:54:39,770] [INFO] Running command: hmmsearch --tblout GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02e0bbc9-7e38-4d51-9552-b2ad45a65f0f/dqc_reference/reference_markers.hmm GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:40,047] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:40,049] [INFO] Found 6/6 markers.
[2024-01-25 18:54:40,098] [INFO] Query marker FASTA was written to GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:54:40,098] [INFO] Task started: Blastn
[2024-01-25 18:54:40,098] [INFO] Running command: blastn -query GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e0bbc9-7e38-4d51-9552-b2ad45a65f0f/dqc_reference/reference_markers.fasta -out GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:41,399] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:41,402] [INFO] Selected 15 target genomes.
[2024-01-25 18:54:41,402] [INFO] Target genome list was writen to GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:54:41,411] [INFO] Task started: fastANI
[2024-01-25 18:54:41,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgee08a70f-382b-46d5-92eb-8d73e4d08b25/GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna.gz --refList GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:01,353] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:01,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02e0bbc9-7e38-4d51-9552-b2ad45a65f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:01,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02e0bbc9-7e38-4d51-9552-b2ad45a65f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:01,364] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:01,364] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:01,364] [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
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	100.0	1994	1995	95	conclusive
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	84.9655	1375	1995	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	84.9637	1362	1995	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	84.9623	1371	1995	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	84.4521	1276	1995	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	84.2535	1317	1995	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	84.1667	1330	1995	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	83.9986	1278	1995	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	82.5675	1179	1995	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	81.5766	1092	1995	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.7397	973	1995	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.3393	966	1995	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.2903	979	1995	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.1418	847	1995	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	80.0236	919	1995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:01,366] [INFO] DFAST Taxonomy check result was written to GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:55:01,366] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:01,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:01,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02e0bbc9-7e38-4d51-9552-b2ad45a65f0f/dqc_reference/checkm_data
[2024-01-25 18:55:01,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:01,423] [INFO] Task started: CheckM
[2024-01-25 18:55:01,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/checkm_input GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:56:28,052] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:28,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:28,077] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:28,077] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:28,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:56:28,079] [INFO] Task started: Blastn
[2024-01-25 18:56:28,079] [INFO] Running command: blastn -query GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e0bbc9-7e38-4d51-9552-b2ad45a65f0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:30,247] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:30,250] [INFO] Selected 20 target genomes.
[2024-01-25 18:56:30,250] [INFO] Target genome list was writen to GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:30,256] [INFO] Task started: fastANI
[2024-01-25 18:56:30,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgee08a70f-382b-46d5-92eb-8d73e4d08b25/GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna.gz --refList GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:57,257] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:57,269] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:57,269] [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_900108565.1	s__Mycobacterium rutilum	100.0	1994	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001722335.1	s__Mycobacterium flavescens_A	88.1441	1556	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	84.9857	1372	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001050015.1	s__Mycobacterium malmesburyense	84.452	1276	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245535.1	s__Mycobacterium lehmannii	84.2971	1311	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCF_001665535.1	s__Mycobacterium sp001665535	84.1999	1305	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001050035.1	s__Mycobacterium komanii	84.1602	1330	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	84.1379	1316	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_001500025.1	s__Mycobacterium sp001500025	83.9709	1286	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637135.1	s__Mycobacterium flavescens	83.8965	1314	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001668575.1	s__Mycobacterium sp001668575	83.8557	1283	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014805.1	s__Mycobacterium elephantis	82.5694	1180	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_010725725.1	s__Mycobacterium pulveris	82.5478	1185	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.1808	972	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086815.1	s__Mycobacterium parafortuitum	81.7181	1151	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001667505.1	s__Mycobacterium sp001667505	81.4861	1178	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000266905.1	s__Mycobacterium chubuense_A	81.4277	1104	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044245.1	s__Mycobacterium obuense	80.9215	990	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
GCF_900637205.1	s__Mycobacterium chitae	80.8417	947	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008329535.1	s__Mycobacterium sp008329535	80.4221	993	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:57,271] [INFO] GTDB search result was written to GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:57,272] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:57,276] [INFO] DFAST_QC result json was written to GCF_900108565.1_IMG-taxon_2636415969_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:56:57,276] [INFO] DFAST_QC completed!
[2024-01-25 18:56:57,276] [INFO] Total running time: 0h2m37s