[2024-01-24 12:31:58,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg11ccd0d9-58fd-40d4-9229-da4d34305567/dqc_reference
[2024-01-24 12:31:59,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,988] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg583d894a-fc2a-482a-babc-325d0f458448/GCF_002983495.1_ASM298349v1_genomic.fna.gz | prodigal -d GCF_002983495.1_ASM298349v1_genomic.fna/cds.fna -a GCF_002983495.1_ASM298349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:16,792] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:16,793] [INFO] Task started: HMMsearch
[2024-01-24 12:32:16,793] [INFO] Running command: hmmsearch --tblout GCF_002983495.1_ASM298349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11ccd0d9-58fd-40d4-9229-da4d34305567/dqc_reference/reference_markers.hmm GCF_002983495.1_ASM298349v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:17,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:17,099] [INFO] Found 6/6 markers.
[2024-01-24 12:32:17,145] [INFO] Query marker FASTA was written to GCF_002983495.1_ASM298349v1_genomic.fna/markers.fasta
[2024-01-24 12:32:17,146] [INFO] Task started: Blastn
[2024-01-24 12:32:17,146] [INFO] Running command: blastn -query GCF_002983495.1_ASM298349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ccd0d9-58fd-40d4-9229-da4d34305567/dqc_reference/reference_markers.fasta -out GCF_002983495.1_ASM298349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:18,374] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:18,379] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:18,379] [INFO] Target genome list was writen to GCF_002983495.1_ASM298349v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:18,387] [INFO] Task started: fastANI
[2024-01-24 12:32:18,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg583d894a-fc2a-482a-babc-325d0f458448/GCF_002983495.1_ASM298349v1_genomic.fna.gz --refList GCF_002983495.1_ASM298349v1_genomic.fna/target_genomes.txt --output GCF_002983495.1_ASM298349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:38,868] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:38,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11ccd0d9-58fd-40d4-9229-da4d34305567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:38,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11ccd0d9-58fd-40d4-9229-da4d34305567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:38,882] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:38,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:38,882] [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 shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	100.0	1714	1714	95	conclusive
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	99.9991	1713	1714	95	conclusive
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	84.1323	1343	1714	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	83.0663	1288	1714	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	82.9403	1196	1714	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	82.934	1298	1714	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	82.7975	1152	1714	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	82.6864	1199	1714	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	82.6745	1180	1714	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	82.3937	1146	1714	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	82.234	1133	1714	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	82.1725	1009	1714	95	below_threshold
Mycobacterium sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	82.144	1186	1714	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	82.029	1059	1714	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	82.0237	1112	1714	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	81.6396	1180	1714	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:38,884] [INFO] DFAST Taxonomy check result was written to GCF_002983495.1_ASM298349v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:38,885] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:38,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:38,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11ccd0d9-58fd-40d4-9229-da4d34305567/dqc_reference/checkm_data
[2024-01-24 12:32:38,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:38,939] [INFO] Task started: CheckM
[2024-01-24 12:32:38,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002983495.1_ASM298349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002983495.1_ASM298349v1_genomic.fna/checkm_input GCF_002983495.1_ASM298349v1_genomic.fna/checkm_result
[2024-01-24 12:33:28,287] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:28,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:28,314] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:28,314] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:28,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002983495.1_ASM298349v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:28,315] [INFO] Task started: Blastn
[2024-01-24 12:33:28,315] [INFO] Running command: blastn -query GCF_002983495.1_ASM298349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ccd0d9-58fd-40d4-9229-da4d34305567/dqc_reference/reference_markers_gtdb.fasta -out GCF_002983495.1_ASM298349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:30,062] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:30,069] [INFO] Selected 21 target genomes.
[2024-01-24 12:33:30,069] [INFO] Target genome list was writen to GCF_002983495.1_ASM298349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:30,085] [INFO] Task started: fastANI
[2024-01-24 12:33:30,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg583d894a-fc2a-482a-babc-325d0f458448/GCF_002983495.1_ASM298349v1_genomic.fna.gz --refList GCF_002983495.1_ASM298349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002983495.1_ASM298349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:56,116] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:56,139] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:56,139] [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_002356315.1	s__Mycobacterium shigaense	99.9991	1713	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.82	1.00	1.00	3	conclusive
GCF_900157375.1	s__Mycobacterium rhizamassiliense	87.0416	1415	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	84.1485	1341	1714	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	83.0459	1292	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	82.7908	1141	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	82.706	1197	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001668725.1	s__Mycobacterium sp001668725	82.6761	1190	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_001667015.1	s__Mycobacterium sp001667015	82.6695	1141	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953985.1	s__Mycobacterium colombiense_B	82.6464	1148	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001667185.1	s__Mycobacterium sp001667185	82.6458	1150	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954195.1	s__Mycobacterium sp001954195	82.5871	1099	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCF_000455205.1	s__Mycobacterium sp000455205	82.5845	1136	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_001954275.1	s__Mycobacterium sp001954275	82.5581	1106	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001672815.1	s__Mycobacterium sp001672815	82.552	1143	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	82.4804	1153	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	82.436	1178	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002104765.1	s__Mycobacterium vulneris	82.4033	1153	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007714205.1	s__Mycobacterium helveticum	82.1645	1010	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002102355.1	s__Mycobacterium sherrisii	82.1428	1186	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	99.78	0.96	0.96	2	-
GCA_004298145.1	s__Mycobacterium sp004298145	81.9455	1094	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727605.1	s__Mycobacterium simiae	81.6429	1180	1714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:56,142] [INFO] GTDB search result was written to GCF_002983495.1_ASM298349v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:56,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:56,147] [INFO] DFAST_QC result json was written to GCF_002983495.1_ASM298349v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:56,147] [INFO] DFAST_QC completed!
[2024-01-24 12:33:56,147] [INFO] Total running time: 0h1m58s