[2024-01-24 13:31:34,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:34,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:34,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c8ea26c-62cb-4752-bdd6-9d572dc03839/dqc_reference
[2024-01-24 13:31:35,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:35,510] [INFO] Task started: Prodigal
[2024-01-24 13:31:35,510] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb739f7f-1f7e-49d8-9614-9de00ff3e2e7/GCF_025821865.1_ASM2582186v1_genomic.fna.gz | prodigal -d GCF_025821865.1_ASM2582186v1_genomic.fna/cds.fna -a GCF_025821865.1_ASM2582186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:46,078] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:46,079] [INFO] Task started: HMMsearch
[2024-01-24 13:31:46,079] [INFO] Running command: hmmsearch --tblout GCF_025821865.1_ASM2582186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c8ea26c-62cb-4752-bdd6-9d572dc03839/dqc_reference/reference_markers.hmm GCF_025821865.1_ASM2582186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:46,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:46,365] [INFO] Found 6/6 markers.
[2024-01-24 13:31:46,398] [INFO] Query marker FASTA was written to GCF_025821865.1_ASM2582186v1_genomic.fna/markers.fasta
[2024-01-24 13:31:46,399] [INFO] Task started: Blastn
[2024-01-24 13:31:46,399] [INFO] Running command: blastn -query GCF_025821865.1_ASM2582186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8ea26c-62cb-4752-bdd6-9d572dc03839/dqc_reference/reference_markers.fasta -out GCF_025821865.1_ASM2582186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:47,813] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:47,816] [INFO] Selected 25 target genomes.
[2024-01-24 13:31:47,816] [INFO] Target genome list was writen to GCF_025821865.1_ASM2582186v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:47,825] [INFO] Task started: fastANI
[2024-01-24 13:31:47,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb739f7f-1f7e-49d8-9614-9de00ff3e2e7/GCF_025821865.1_ASM2582186v1_genomic.fna.gz --refList GCF_025821865.1_ASM2582186v1_genomic.fna/target_genomes.txt --output GCF_025821865.1_ASM2582186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:12,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:12,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c8ea26c-62cb-4752-bdd6-9d572dc03839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:12,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c8ea26c-62cb-4752-bdd6-9d572dc03839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:12,201] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:12,201] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:12,202] [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
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	81.2113	698	1104	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.1522	670	1104	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.1336	681	1104	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	81.0951	698	1104	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.0616	684	1104	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	80.9979	713	1104	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	80.9939	691	1104	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	80.992	692	1104	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	80.9906	668	1104	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	80.9462	711	1104	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	80.9449	698	1104	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	80.9103	713	1104	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	80.4938	667	1104	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.4157	644	1104	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	80.4063	661	1104	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	80.3661	630	1104	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	80.3335	645	1104	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	80.283	641	1104	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	80.223	664	1104	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.1737	628	1104	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	80.1476	668	1104	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	80.0902	635	1104	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	79.5988	593	1104	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	79.5868	584	1104	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	79.5453	591	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:12,207] [INFO] DFAST Taxonomy check result was written to GCF_025821865.1_ASM2582186v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:12,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:12,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:12,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c8ea26c-62cb-4752-bdd6-9d572dc03839/dqc_reference/checkm_data
[2024-01-24 13:32:12,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:12,251] [INFO] Task started: CheckM
[2024-01-24 13:32:12,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821865.1_ASM2582186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821865.1_ASM2582186v1_genomic.fna/checkm_input GCF_025821865.1_ASM2582186v1_genomic.fna/checkm_result
[2024-01-24 13:32:46,989] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:46,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:47,004] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:47,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:47,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821865.1_ASM2582186v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:47,006] [INFO] Task started: Blastn
[2024-01-24 13:32:47,006] [INFO] Running command: blastn -query GCF_025821865.1_ASM2582186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8ea26c-62cb-4752-bdd6-9d572dc03839/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821865.1_ASM2582186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:49,396] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,400] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:49,400] [INFO] Target genome list was writen to GCF_025821865.1_ASM2582186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:49,461] [INFO] Task started: fastANI
[2024-01-24 13:32:49,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb739f7f-1f7e-49d8-9614-9de00ff3e2e7/GCF_025821865.1_ASM2582186v1_genomic.fna.gz --refList GCF_025821865.1_ASM2582186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821865.1_ASM2582186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:06,254] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:06,273] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:06,273] [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_002102395.1	s__Mycobacterium triviale	99.9778	1084	1104	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_001668625.1	s__Mycobacterium sp001668625	90.3133	958	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104795.1	s__Mycobacterium koreense	83.7928	876	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	98.84	0.96	0.92	3	-
GCF_018455725.1	s__Mycobacterium sp018455725	81.5296	708	1104	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	81.1033	684	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001667945.1	s__Mycobacterium sinense_B	81.0504	702	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_002086455.1	s__Mycobacterium algericum	81.0386	701	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_002086285.1	s__Mycobacterium kumamotonense	80.9675	717	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_002101585.1	s__Mycobacterium engbaekii	80.506	666	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	80.3408	644	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001494595.1	s__Mycobacterium sp001494595	80.3198	630	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	80.2841	654	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	80.243	684	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_900240975.1	s__Mycobacterium sp900240975	80.2208	645	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	80.0779	666	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689175.1	s__Mycobacterium kubicae	79.537	592	1104	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:06,275] [INFO] GTDB search result was written to GCF_025821865.1_ASM2582186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:06,276] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:06,280] [INFO] DFAST_QC result json was written to GCF_025821865.1_ASM2582186v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:06,280] [INFO] DFAST_QC completed!
[2024-01-24 13:33:06,280] [INFO] Total running time: 0h1m32s