[2024-01-24 13:40:35,121] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgd28f34c0-b136-4d22-b9e5-30c4afa774f8/dqc_reference
[2024-01-24 13:40:36,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,440] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,441] [INFO] Running command: gunzip -c /var/lib/cwl/stg20e58e53-b016-4bb4-9b31-69bd84fc5398/GCF_002101995.1_ASM210199v1_genomic.fna.gz | prodigal -d GCF_002101995.1_ASM210199v1_genomic.fna/cds.fna -a GCF_002101995.1_ASM210199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,111] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,111] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,111] [INFO] Running command: hmmsearch --tblout GCF_002101995.1_ASM210199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd28f34c0-b136-4d22-b9e5-30c4afa774f8/dqc_reference/reference_markers.hmm GCF_002101995.1_ASM210199v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,415] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,463] [INFO] Query marker FASTA was written to GCF_002101995.1_ASM210199v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,464] [INFO] Task started: Blastn
[2024-01-24 13:40:49,464] [INFO] Running command: blastn -query GCF_002101995.1_ASM210199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd28f34c0-b136-4d22-b9e5-30c4afa774f8/dqc_reference/reference_markers.fasta -out GCF_002101995.1_ASM210199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,756] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,760] [INFO] Selected 12 target genomes.
[2024-01-24 13:40:50,760] [INFO] Target genome list was writen to GCF_002101995.1_ASM210199v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,767] [INFO] Task started: fastANI
[2024-01-24 13:40:50,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg20e58e53-b016-4bb4-9b31-69bd84fc5398/GCF_002101995.1_ASM210199v1_genomic.fna.gz --refList GCF_002101995.1_ASM210199v1_genomic.fna/target_genomes.txt --output GCF_002101995.1_ASM210199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,981] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd28f34c0-b136-4d22-b9e5-30c4afa774f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd28f34c0-b136-4d22-b9e5-30c4afa774f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,992] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:05,992] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:05,992] [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 fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	100.0	1358	1368	95	conclusive
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	99.9679	1326	1368	95	conclusive
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	84.3113	997	1368	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	84.0706	830	1368	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	83.9327	862	1368	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	81.8918	860	1368	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	81.7702	869	1368	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.4147	813	1368	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.4145	801	1368	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.3412	805	1368	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.5247	798	1368	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.4563	764	1368	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,994] [INFO] DFAST Taxonomy check result was written to GCF_002101995.1_ASM210199v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,995] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,995] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd28f34c0-b136-4d22-b9e5-30c4afa774f8/dqc_reference/checkm_data
[2024-01-24 13:41:05,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:06,043] [INFO] Task started: CheckM
[2024-01-24 13:41:06,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101995.1_ASM210199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101995.1_ASM210199v1_genomic.fna/checkm_input GCF_002101995.1_ASM210199v1_genomic.fna/checkm_result
[2024-01-24 13:41:49,908] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:49,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,927] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:49,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:49,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101995.1_ASM210199v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:49,929] [INFO] Task started: Blastn
[2024-01-24 13:41:49,929] [INFO] Running command: blastn -query GCF_002101995.1_ASM210199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd28f34c0-b136-4d22-b9e5-30c4afa774f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101995.1_ASM210199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,898] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:51,898] [INFO] Target genome list was writen to GCF_002101995.1_ASM210199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:51,910] [INFO] Task started: fastANI
[2024-01-24 13:41:51,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg20e58e53-b016-4bb4-9b31-69bd84fc5398/GCF_002101995.1_ASM210199v1_genomic.fna.gz --refList GCF_002101995.1_ASM210199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101995.1_ASM210199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:10,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:10,800] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:10,800] [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_010726955.1	s__Mycobacterium fallax	99.9679	1326	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	conclusive
GCF_010731615.1	s__Mycobacterium insubricum	84.3431	994	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004014795.1	s__Mycobacterium brumae	84.0387	833	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.98	0.98	0.98	3	-
GCF_001583415.1	s__Mycobacterium phlei	81.3643	819	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_002592005.1	s__Mycobacterium palauense	81.3509	831	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668625.1	s__Mycobacterium sp001668625	81.2478	695	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102395.1	s__Mycobacterium triviale	81.071	672	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018455725.1	s__Mycobacterium sp018455725	80.869	699	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727125.1	s__Mycobacterium terrae	80.7465	706	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000613185.1	s__Mycobacterium cosmeticum	80.6213	777	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_011758805.1	s__Mycobacterium fluoranthenivorans	80.3665	750	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	-
GCF_001667945.1	s__Mycobacterium sinense_B	80.3611	692	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_001457595.1	s__Mycobacterium smegmatis	80.3093	744	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_002086455.1	s__Mycobacterium algericum	80.2276	729	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_001666755.1	s__Mycobacterium sp001666755	79.8735	685	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.50	99.03	0.96	0.95	3	-
GCF_002798385.1	s__Mycobacterium goodii	79.7753	704	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	79.7217	714	1368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,802] [INFO] GTDB search result was written to GCF_002101995.1_ASM210199v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:10,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:10,806] [INFO] DFAST_QC result json was written to GCF_002101995.1_ASM210199v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:10,806] [INFO] DFAST_QC completed!
[2024-01-24 13:42:10,806] [INFO] Total running time: 0h1m36s