[2024-01-25 17:38:35,377] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:35,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:35,380] [INFO] DQC Reference Directory: /var/lib/cwl/stged0191c1-7dce-4294-aca4-472e43784c27/dqc_reference
[2024-01-25 17:38:36,473] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:36,474] [INFO] Task started: Prodigal
[2024-01-25 17:38:36,474] [INFO] Running command: gunzip -c /var/lib/cwl/stg926f8922-030a-4fc8-9f2c-2944d75e6adf/GCF_025822475.1_ASM2582247v1_genomic.fna.gz | prodigal -d GCF_025822475.1_ASM2582247v1_genomic.fna/cds.fna -a GCF_025822475.1_ASM2582247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:57,960] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:57,960] [INFO] Task started: HMMsearch
[2024-01-25 17:38:57,960] [INFO] Running command: hmmsearch --tblout GCF_025822475.1_ASM2582247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged0191c1-7dce-4294-aca4-472e43784c27/dqc_reference/reference_markers.hmm GCF_025822475.1_ASM2582247v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:58,287] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:58,288] [INFO] Found 6/6 markers.
[2024-01-25 17:38:58,348] [INFO] Query marker FASTA was written to GCF_025822475.1_ASM2582247v1_genomic.fna/markers.fasta
[2024-01-25 17:38:58,349] [INFO] Task started: Blastn
[2024-01-25 17:38:58,349] [INFO] Running command: blastn -query GCF_025822475.1_ASM2582247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged0191c1-7dce-4294-aca4-472e43784c27/dqc_reference/reference_markers.fasta -out GCF_025822475.1_ASM2582247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:59,523] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:59,531] [INFO] Selected 27 target genomes.
[2024-01-25 17:38:59,532] [INFO] Target genome list was writen to GCF_025822475.1_ASM2582247v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:59,535] [INFO] Task started: fastANI
[2024-01-25 17:38:59,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg926f8922-030a-4fc8-9f2c-2944d75e6adf/GCF_025822475.1_ASM2582247v1_genomic.fna.gz --refList GCF_025822475.1_ASM2582247v1_genomic.fna/target_genomes.txt --output GCF_025822475.1_ASM2582247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:35,901] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:35,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged0191c1-7dce-4294-aca4-472e43784c27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:35,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged0191c1-7dce-4294-aca4-472e43784c27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:35,917] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:35,917] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:35,917] [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 wolinskyi	strain=ATCC 700010	GCA_002101965.1	59750	59750	type	True	99.9935	2457	2477	95	conclusive
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	82.6567	1601	2477	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	82.6016	1604	2477	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	82.4706	1368	2477	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	82.466	1373	2477	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	82.4056	1394	2477	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	82.3914	1355	2477	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	82.2842	1458	2477	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	82.2621	1376	2477	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	82.2468	1395	2477	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	82.1586	1211	2477	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	81.9762	1302	2477	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	81.9604	1306	2477	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	81.8588	1356	2477	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	81.8379	1291	2477	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	81.8136	1182	2477	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	81.7644	1288	2477	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	81.7428	1376	2477	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.0335	1041	2477	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.6024	836	2477	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5712	902	2477	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5335	911	2477	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	79.3706	687	2477	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	79.024	667	2477	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	78.9407	663	2477	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	78.9348	656	2477	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	78.8582	702	2477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:35,920] [INFO] DFAST Taxonomy check result was written to GCF_025822475.1_ASM2582247v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:35,920] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:35,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:35,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged0191c1-7dce-4294-aca4-472e43784c27/dqc_reference/checkm_data
[2024-01-25 17:39:35,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:35,994] [INFO] Task started: CheckM
[2024-01-25 17:39:35,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822475.1_ASM2582247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822475.1_ASM2582247v1_genomic.fna/checkm_input GCF_025822475.1_ASM2582247v1_genomic.fna/checkm_result
[2024-01-25 17:40:52,535] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:52,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:52,560] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:52,561] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:52,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822475.1_ASM2582247v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:52,562] [INFO] Task started: Blastn
[2024-01-25 17:40:52,562] [INFO] Running command: blastn -query GCF_025822475.1_ASM2582247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged0191c1-7dce-4294-aca4-472e43784c27/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822475.1_ASM2582247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:54,530] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:54,533] [INFO] Selected 23 target genomes.
[2024-01-25 17:40:54,533] [INFO] Target genome list was writen to GCF_025822475.1_ASM2582247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:54,545] [INFO] Task started: fastANI
[2024-01-25 17:40:54,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg926f8922-030a-4fc8-9f2c-2944d75e6adf/GCF_025822475.1_ASM2582247v1_genomic.fna.gz --refList GCF_025822475.1_ASM2582247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822475.1_ASM2582247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:27,350] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:27,363] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:27,364] [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_002101965.1	s__Mycobacterium wolinskyi	99.9935	2457	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.70	97.70	0.86	0.86	2	conclusive
GCF_001187505.1	s__Mycobacterium goodii_B	82.6712	1455	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	82.6501	1603	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_900078665.2	s__Mycobacterium houstonense	82.4796	1366	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457595.1	s__Mycobacterium smegmatis	82.4728	1418	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_002798385.1	s__Mycobacterium goodii	82.4065	1417	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_000455325.1	s__Mycobacterium septicum	82.3867	1398	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_009729095.1	s__Mycobacterium sp009729095	82.2713	1269	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_001245615.1	s__Mycobacterium neworleansense	82.2694	1375	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762045.1	s__Mycobacterium sp004762045	82.2539	1326	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731295.1	s__Mycobacterium boenickei	82.2485	1395	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001942045.1	s__Mycobacterium porcinum_A	82.1698	1317	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019050325.1	s__Mycobacterium fortunisiensis	82.1571	1212	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086835.1	s__Mycobacterium porcinum	82.0909	1417	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_000805385.1	s__Mycobacterium setense	81.983	1302	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	98.47	0.95	0.89	4	-
GCF_000723385.1	s__Mycobacterium farcinogenes	81.8997	1337	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	-
GCF_001570425.1	s__Mycobacterium brisbanense	81.7908	1356	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.59	97.59	0.86	0.86	2	-
GCF_000295855.1	s__Mycobacterium fortuitum	81.7573	1288	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.3234	918	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644575.1	s__Mycobacterium sp001644575	79.8572	988	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_003284935.1	s__Mycobacterium arosiense_A	79.5855	735	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086125.1	s__Mycobacterium arosiense	78.8571	702	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689255.1	s__Mycobacterium triplex	78.8268	754	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:27,365] [INFO] GTDB search result was written to GCF_025822475.1_ASM2582247v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:27,366] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:27,370] [INFO] DFAST_QC result json was written to GCF_025822475.1_ASM2582247v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:27,370] [INFO] DFAST_QC completed!
[2024-01-25 17:41:27,370] [INFO] Total running time: 0h2m52s