[2024-01-25 18:09:05,609] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:05,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:05,614] [INFO] DQC Reference Directory: /var/lib/cwl/stga907a8eb-6b33-4215-b6dd-d656c94255b4/dqc_reference
[2024-01-25 18:09:06,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:06,793] [INFO] Task started: Prodigal
[2024-01-25 18:09:06,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b323aab-4bc2-414f-ad9b-1ba8fcfd37f1/GCF_022430545.2_ASM2243054v2_genomic.fna.gz | prodigal -d GCF_022430545.2_ASM2243054v2_genomic.fna/cds.fna -a GCF_022430545.2_ASM2243054v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:23,575] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:23,576] [INFO] Task started: HMMsearch
[2024-01-25 18:09:23,576] [INFO] Running command: hmmsearch --tblout GCF_022430545.2_ASM2243054v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga907a8eb-6b33-4215-b6dd-d656c94255b4/dqc_reference/reference_markers.hmm GCF_022430545.2_ASM2243054v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:23,817] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:23,818] [INFO] Found 6/6 markers.
[2024-01-25 18:09:23,862] [INFO] Query marker FASTA was written to GCF_022430545.2_ASM2243054v2_genomic.fna/markers.fasta
[2024-01-25 18:09:23,863] [INFO] Task started: Blastn
[2024-01-25 18:09:23,863] [INFO] Running command: blastn -query GCF_022430545.2_ASM2243054v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga907a8eb-6b33-4215-b6dd-d656c94255b4/dqc_reference/reference_markers.fasta -out GCF_022430545.2_ASM2243054v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:24,933] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:24,936] [INFO] Selected 25 target genomes.
[2024-01-25 18:09:24,937] [INFO] Target genome list was writen to GCF_022430545.2_ASM2243054v2_genomic.fna/target_genomes.txt
[2024-01-25 18:09:24,955] [INFO] Task started: fastANI
[2024-01-25 18:09:24,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b323aab-4bc2-414f-ad9b-1ba8fcfd37f1/GCF_022430545.2_ASM2243054v2_genomic.fna.gz --refList GCF_022430545.2_ASM2243054v2_genomic.fna/target_genomes.txt --output GCF_022430545.2_ASM2243054v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:51,601] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:51,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga907a8eb-6b33-4215-b6dd-d656c94255b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:51,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga907a8eb-6b33-4215-b6dd-d656c94255b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:51,619] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:09:51,620] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:09:51,620] [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
Mycobacterium cookii	strain=JCM 12404	GCA_010727945.1	1775	1775	type	True	81.7851	1137	1840	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	80.1836	822	1840	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	80.1816	888	1840	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.0321	869	1840	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	79.8165	820	1840	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	79.7992	836	1840	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	79.7712	828	1840	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	79.7644	842	1840	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	79.7641	806	1840	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	79.7481	808	1840	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	79.7143	822	1840	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	79.6953	797	1840	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	79.6792	824	1840	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	79.6766	836	1840	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	79.6512	773	1840	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	79.5942	783	1840	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	79.577	799	1840	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	79.3933	830	1840	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	79.3914	809	1840	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	79.2683	753	1840	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	78.8155	698	1840	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	78.8117	649	1840	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	78.7051	634	1840	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	78.6719	712	1840	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	78.498	640	1840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:51,623] [INFO] DFAST Taxonomy check result was written to GCF_022430545.2_ASM2243054v2_genomic.fna/tc_result.tsv
[2024-01-25 18:09:51,624] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:51,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:51,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga907a8eb-6b33-4215-b6dd-d656c94255b4/dqc_reference/checkm_data
[2024-01-25 18:09:51,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:51,691] [INFO] Task started: CheckM
[2024-01-25 18:09:51,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022430545.2_ASM2243054v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022430545.2_ASM2243054v2_genomic.fna/checkm_input GCF_022430545.2_ASM2243054v2_genomic.fna/checkm_result
[2024-01-25 18:10:45,012] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:45,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:45,033] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:45,034] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:45,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022430545.2_ASM2243054v2_genomic.fna/markers.fasta)
[2024-01-25 18:10:45,036] [INFO] Task started: Blastn
[2024-01-25 18:10:45,036] [INFO] Running command: blastn -query GCF_022430545.2_ASM2243054v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga907a8eb-6b33-4215-b6dd-d656c94255b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_022430545.2_ASM2243054v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:46,622] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:46,624] [INFO] Selected 19 target genomes.
[2024-01-25 18:10:46,624] [INFO] Target genome list was writen to GCF_022430545.2_ASM2243054v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:46,639] [INFO] Task started: fastANI
[2024-01-25 18:10:46,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b323aab-4bc2-414f-ad9b-1ba8fcfd37f1/GCF_022430545.2_ASM2243054v2_genomic.fna.gz --refList GCF_022430545.2_ASM2243054v2_genomic.fna/target_genomes_gtdb.txt --output GCF_022430545.2_ASM2243054v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:09,289] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:09,300] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:11:09,300] [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_001673405.1	s__Mycobacterium sp001673405	84.7905	1360	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863225.1	s__Mycobacterium sp002863225	82.8334	1216	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727945.1	s__Mycobacterium cookii	81.7886	1133	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001666755.1	s__Mycobacterium sp001666755	80.3568	814	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.50	99.03	0.96	0.95	3	-
GCF_001673535.1	s__Mycobacterium sp001673535	79.9233	837	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	79.911	823	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_001667885.1	s__Mycobacterium scrofulaceum_C	79.8271	823	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.31	98.31	0.93	0.93	2	-
GCF_001668725.1	s__Mycobacterium sp001668725	79.7974	850	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_002102185.1	s__Mycobacterium fragae	79.7813	826	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731775.1	s__Mycobacterium mantenii	79.7143	820	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_001053185.1	s__Mycobacterium bohemicum	79.7142	794	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_002102155.1	s__Mycobacterium europaeum	79.6334	840	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001667035.1	s__Mycobacterium sp001667035	79.5839	792	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176255.2	s__Mycobacterium ahvazicum	79.562	801	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240975.1	s__Mycobacterium sp900240975	79.5496	818	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_010729105.1	s__Mycobacterium saskatchewanense	79.4	829	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_019243155.1	s__Mycobacterium sp019243155	79.3146	667	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426065.1	s__Mycobacterium sp000426065	78.5128	640	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805385.1	s__Mycobacterium setense	78.4913	641	1840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	98.47	0.95	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:09,301] [INFO] GTDB search result was written to GCF_022430545.2_ASM2243054v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:09,302] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:09,306] [INFO] DFAST_QC result json was written to GCF_022430545.2_ASM2243054v2_genomic.fna/dqc_result.json
[2024-01-25 18:11:09,306] [INFO] DFAST_QC completed!
[2024-01-25 18:11:09,306] [INFO] Total running time: 0h2m4s