[2024-01-24 11:51:49,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:49,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:49,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg36c7e6bd-80ad-4815-a7d1-537bb9a75c53/dqc_reference
[2024-01-24 11:51:51,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,018] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,018] [INFO] Running command: gunzip -c /var/lib/cwl/stgab64596d-5c9d-4909-b0cf-6e4f2e79ec99/GCF_002116635.1_ASM211663v1_genomic.fna.gz | prodigal -d GCF_002116635.1_ASM211663v1_genomic.fna/cds.fna -a GCF_002116635.1_ASM211663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:15,094] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:15,095] [INFO] Task started: HMMsearch
[2024-01-24 11:52:15,095] [INFO] Running command: hmmsearch --tblout GCF_002116635.1_ASM211663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36c7e6bd-80ad-4815-a7d1-537bb9a75c53/dqc_reference/reference_markers.hmm GCF_002116635.1_ASM211663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:15,418] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:15,420] [INFO] Found 6/6 markers.
[2024-01-24 11:52:15,477] [INFO] Query marker FASTA was written to GCF_002116635.1_ASM211663v1_genomic.fna/markers.fasta
[2024-01-24 11:52:15,477] [INFO] Task started: Blastn
[2024-01-24 11:52:15,477] [INFO] Running command: blastn -query GCF_002116635.1_ASM211663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36c7e6bd-80ad-4815-a7d1-537bb9a75c53/dqc_reference/reference_markers.fasta -out GCF_002116635.1_ASM211663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:16,584] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:16,588] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:16,589] [INFO] Target genome list was writen to GCF_002116635.1_ASM211663v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:16,602] [INFO] Task started: fastANI
[2024-01-24 11:52:16,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgab64596d-5c9d-4909-b0cf-6e4f2e79ec99/GCF_002116635.1_ASM211663v1_genomic.fna.gz --refList GCF_002116635.1_ASM211663v1_genomic.fna/target_genomes.txt --output GCF_002116635.1_ASM211663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:44,657] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:44,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36c7e6bd-80ad-4815-a7d1-537bb9a75c53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:44,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36c7e6bd-80ad-4815-a7d1-537bb9a75c53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:44,682] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:44,682] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:44,682] [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 szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	100.0	2130	2135	95	conclusive
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	93.1125	1835	2135	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	81.7324	1132	2135	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	81.6772	1169	2135	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	81.3901	1228	2135	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	81.2227	1197	2135	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	81.1835	1148	2135	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	81.1678	1053	2135	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	81.1668	1058	2135	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	81.1282	1062	2135	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	80.8864	1210	2135	95	below_threshold
Mycobacterium attenuatum	strain=MK41	GCA_900566085.1	2341086	2341086	type	True	80.794	1127	2135	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	80.6679	1023	2135	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	80.6533	1017	2135	95	below_threshold
Mycobacterium vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	80.3441	1047	2135	95	below_threshold
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_001515365.1	265949	265949	suspected-type	True	80.2747	1050	2135	95	below_threshold
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_003584745.1	265949	265949	suspected-type	True	80.2354	1076	2135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:44,684] [INFO] DFAST Taxonomy check result was written to GCF_002116635.1_ASM211663v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:44,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:44,685] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:44,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36c7e6bd-80ad-4815-a7d1-537bb9a75c53/dqc_reference/checkm_data
[2024-01-24 11:52:44,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:44,751] [INFO] Task started: CheckM
[2024-01-24 11:52:44,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002116635.1_ASM211663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002116635.1_ASM211663v1_genomic.fna/checkm_input GCF_002116635.1_ASM211663v1_genomic.fna/checkm_result
[2024-01-24 11:53:50,016] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:50,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:50,043] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:50,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:50,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002116635.1_ASM211663v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:50,044] [INFO] Task started: Blastn
[2024-01-24 11:53:50,044] [INFO] Running command: blastn -query GCF_002116635.1_ASM211663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36c7e6bd-80ad-4815-a7d1-537bb9a75c53/dqc_reference/reference_markers_gtdb.fasta -out GCF_002116635.1_ASM211663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:51,570] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:51,575] [INFO] Selected 20 target genomes.
[2024-01-24 11:53:51,575] [INFO] Target genome list was writen to GCF_002116635.1_ASM211663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:51,589] [INFO] Task started: fastANI
[2024-01-24 11:53:51,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgab64596d-5c9d-4909-b0cf-6e4f2e79ec99/GCF_002116635.1_ASM211663v1_genomic.fna.gz --refList GCF_002116635.1_ASM211663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002116635.1_ASM211663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:23,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:23,511] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:23,511] [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_002116635.1	s__Mycobacterium szulgai	100.0	2130	2135	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_002086155.1	s__Mycobacterium angelicum	93.1148	1835	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731535.1	s__Mycobacterium lacus	81.6667	1168	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	81.4007	1224	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.193	1204	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_002086675.1	s__Mycobacterium persicum	81.1777	1149	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_900078675.2	s__Mycobacterium interjectum	81.1727	1091	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.1701	1113	2135	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	81.1648	1059	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCF_002104675.1	s__Mycobacterium decipiens	81.0388	1103	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673635.1	s__Mycobacterium asiaticum_C	80.9413	1102	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_002101675.1	s__Mycobacterium gordonae	80.8988	1210	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_001673155.1	s__Mycobacterium sp001673155	80.8343	965	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247635.1	s__Mycobacterium sp019247635	80.8085	956	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566085.1	s__Mycobacterium attenuatum	80.7893	1125	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.59	99.54	0.94	0.93	4	-
GCF_001417955.2	s__Mycobacterium gordonae_B	80.7687	1177	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	80.6647	994	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_010731675.1	s__Mycobacterium marseillense	80.639	1029	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_017086405.1	s__Mycobacterium gordonae_D	80.5424	1209	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466425.1	s__Mycobacterium vicinigordonae	80.315	1056	2135	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 11:54:23,513] [INFO] GTDB search result was written to GCF_002116635.1_ASM211663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:23,514] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:23,518] [INFO] DFAST_QC result json was written to GCF_002116635.1_ASM211663v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:23,518] [INFO] DFAST_QC completed!
[2024-01-24 11:54:23,518] [INFO] Total running time: 0h2m34s