[2023-06-13 12:39:08,300] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:39:08,302] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:39:08,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg58508c39-39bd-4041-bf17-6dfd30eaafdc/dqc_reference
[2023-06-13 12:39:09,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:39:09,512] [INFO] Task started: Prodigal
[2023-06-13 12:39:09,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg38b0ef04-1c74-491d-84a9-4d17d618a7b1/GCA_022600855.1_ASM2260085v1_genomic.fna.gz | prodigal -d GCA_022600855.1_ASM2260085v1_genomic.fna/cds.fna -a GCA_022600855.1_ASM2260085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:39:18,230] [INFO] Task succeeded: Prodigal
[2023-06-13 12:39:18,231] [INFO] Task started: HMMsearch
[2023-06-13 12:39:18,231] [INFO] Running command: hmmsearch --tblout GCA_022600855.1_ASM2260085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58508c39-39bd-4041-bf17-6dfd30eaafdc/dqc_reference/reference_markers.hmm GCA_022600855.1_ASM2260085v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:39:18,461] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:39:18,462] [INFO] Found 6/6 markers.
[2023-06-13 12:39:18,495] [INFO] Query marker FASTA was written to GCA_022600855.1_ASM2260085v1_genomic.fna/markers.fasta
[2023-06-13 12:39:18,495] [INFO] Task started: Blastn
[2023-06-13 12:39:18,495] [INFO] Running command: blastn -query GCA_022600855.1_ASM2260085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58508c39-39bd-4041-bf17-6dfd30eaafdc/dqc_reference/reference_markers.fasta -out GCA_022600855.1_ASM2260085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:39:19,509] [INFO] Task succeeded: Blastn
[2023-06-13 12:39:19,514] [INFO] Selected 24 target genomes.
[2023-06-13 12:39:19,515] [INFO] Target genome list was writen to GCA_022600855.1_ASM2260085v1_genomic.fna/target_genomes.txt
[2023-06-13 12:39:19,525] [INFO] Task started: fastANI
[2023-06-13 12:39:19,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b0ef04-1c74-491d-84a9-4d17d618a7b1/GCA_022600855.1_ASM2260085v1_genomic.fna.gz --refList GCA_022600855.1_ASM2260085v1_genomic.fna/target_genomes.txt --output GCA_022600855.1_ASM2260085v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:39:40,467] [INFO] Task succeeded: fastANI
[2023-06-13 12:39:40,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58508c39-39bd-4041-bf17-6dfd30eaafdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:39:40,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58508c39-39bd-4041-bf17-6dfd30eaafdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:39:40,490] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:39:40,490] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 12:39:40,490] [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 psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	79.7608	569	937	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	79.7534	572	937	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	79.74	578	937	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	79.7357	587	937	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	79.7286	574	937	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	79.7025	575	937	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	79.6135	517	937	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	79.5692	555	937	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	79.5562	552	937	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	79.5495	547	937	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	78.6547	339	937	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	78.5636	422	937	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	78.5141	436	937	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	78.5088	393	937	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	78.4786	447	937	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	78.4756	399	937	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	78.3946	427	937	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	78.3869	352	937	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	78.3653	360	937	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	78.3382	433	937	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	78.2848	443	937	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	78.2437	335	937	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	77.9917	395	937	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	77.9174	330	937	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:39:40,492] [INFO] DFAST Taxonomy check result was written to GCA_022600855.1_ASM2260085v1_genomic.fna/tc_result.tsv
[2023-06-13 12:39:40,493] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:39:40,493] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:39:40,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58508c39-39bd-4041-bf17-6dfd30eaafdc/dqc_reference/checkm_data
[2023-06-13 12:39:40,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:39:40,528] [INFO] Task started: CheckM
[2023-06-13 12:39:40,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022600855.1_ASM2260085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022600855.1_ASM2260085v1_genomic.fna/checkm_input GCA_022600855.1_ASM2260085v1_genomic.fna/checkm_result
[2023-06-13 12:40:10,952] [INFO] Task succeeded: CheckM
[2023-06-13 12:40:10,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 3.82%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 12:40:10,980] [INFO] ===== Completeness check finished =====
[2023-06-13 12:40:10,981] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:40:10,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022600855.1_ASM2260085v1_genomic.fna/markers.fasta)
[2023-06-13 12:40:10,981] [INFO] Task started: Blastn
[2023-06-13 12:40:10,981] [INFO] Running command: blastn -query GCA_022600855.1_ASM2260085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58508c39-39bd-4041-bf17-6dfd30eaafdc/dqc_reference/reference_markers_gtdb.fasta -out GCA_022600855.1_ASM2260085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:40:12,360] [INFO] Task succeeded: Blastn
[2023-06-13 12:40:12,366] [INFO] Selected 20 target genomes.
[2023-06-13 12:40:12,366] [INFO] Target genome list was writen to GCA_022600855.1_ASM2260085v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:40:12,383] [INFO] Task started: fastANI
[2023-06-13 12:40:12,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b0ef04-1c74-491d-84a9-4d17d618a7b1/GCA_022600855.1_ASM2260085v1_genomic.fna.gz --refList GCA_022600855.1_ASM2260085v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022600855.1_ASM2260085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:40:32,050] [INFO] Task succeeded: fastANI
[2023-06-13 12:40:32,073] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 12:40:32,073] [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_013390125.1	s__Mycobacterium hippocampi_A	81.1422	689	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	81.132	703	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705885.1	s__Mycobacterium vanbaalenii_A	81.0516	687	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222675.1	s__Mycobacterium sp005222675	80.9299	678	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	79.7674	609	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_000266905.1	s__Mycobacterium chubuense_A	79.7301	588	937	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	79.6738	496	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	79.593	518	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_017312405.1	s__Mycobacterium sp017312405	79.4312	541	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900454025.1	s__Mycobacterium gilvum	79.3122	548	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_010728325.1	s__Mycobacterium poriferae	79.2804	570	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.01	98.01	0.88	0.88	2	-
GCF_001499995.1	s__Mycobacterium sp001499995	78.9015	452	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329645.1	s__Mycobacterium grossiae	78.6446	420	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.93	99.93	0.94	0.94	2	-
GCF_001667505.1	s__Mycobacterium sp001667505	78.5903	479	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731815.2	s__Mycobacterium arabiense	78.5533	423	937	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	78.5075	434	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	78.4855	398	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_016313185.1	s__Mycobacterium sp016313185	78.4697	448	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_010731615.1	s__Mycobacterium insubricum	78.237	335	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903884065.1	s__Mycobacterium sp903884065	77.8055	312	937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-13 12:40:32,076] [INFO] GTDB search result was written to GCA_022600855.1_ASM2260085v1_genomic.fna/result_gtdb.tsv
[2023-06-13 12:40:32,076] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:40:32,081] [INFO] DFAST_QC result json was written to GCA_022600855.1_ASM2260085v1_genomic.fna/dqc_result.json
[2023-06-13 12:40:32,081] [INFO] DFAST_QC completed!
[2023-06-13 12:40:32,082] [INFO] Total running time: 0h1m24s