[2024-01-24 10:47:24,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,717] [INFO] DQC Reference Directory: /var/lib/cwl/stge1e6671d-ce45-4ddd-afcc-9505641cff66/dqc_reference
[2024-01-24 10:47:26,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,597] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg174d575e-7573-420b-b461-bcb93049e72b/GCF_019710635.1_ASM1971063v1_genomic.fna.gz | prodigal -d GCF_019710635.1_ASM1971063v1_genomic.fna/cds.fna -a GCF_019710635.1_ASM1971063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:43,204] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:43,205] [INFO] Task started: HMMsearch
[2024-01-24 10:47:43,205] [INFO] Running command: hmmsearch --tblout GCF_019710635.1_ASM1971063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1e6671d-ce45-4ddd-afcc-9505641cff66/dqc_reference/reference_markers.hmm GCF_019710635.1_ASM1971063v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:43,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:43,518] [INFO] Found 6/6 markers.
[2024-01-24 10:47:43,566] [INFO] Query marker FASTA was written to GCF_019710635.1_ASM1971063v1_genomic.fna/markers.fasta
[2024-01-24 10:47:43,566] [INFO] Task started: Blastn
[2024-01-24 10:47:43,566] [INFO] Running command: blastn -query GCF_019710635.1_ASM1971063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1e6671d-ce45-4ddd-afcc-9505641cff66/dqc_reference/reference_markers.fasta -out GCF_019710635.1_ASM1971063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:44,732] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:44,736] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:44,736] [INFO] Target genome list was writen to GCF_019710635.1_ASM1971063v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:44,745] [INFO] Task started: fastANI
[2024-01-24 10:47:44,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg174d575e-7573-420b-b461-bcb93049e72b/GCF_019710635.1_ASM1971063v1_genomic.fna.gz --refList GCF_019710635.1_ASM1971063v1_genomic.fna/target_genomes.txt --output GCF_019710635.1_ASM1971063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:04,899] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:04,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1e6671d-ce45-4ddd-afcc-9505641cff66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:04,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1e6671d-ce45-4ddd-afcc-9505641cff66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:04,917] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:04,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:04,918] [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 chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	82.6996	1126	1793	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	82.665	1127	1793	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	82.6444	1112	1793	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	82.5686	1002	1793	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	82.5638	1091	1793	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	82.5617	1122	1793	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	82.5576	1131	1793	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	82.5354	1094	1793	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.8537	988	1793	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.7933	1002	1793	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.7518	1019	1793	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.5338	1070	1793	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.5252	1076	1793	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.5283	660	1793	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	79.0152	615	1793	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	79.0061	624	1793	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	78.5215	591	1793	95	below_threshold
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	78.0767	463	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,920] [INFO] DFAST Taxonomy check result was written to GCF_019710635.1_ASM1971063v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:04,921] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:04,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:04,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1e6671d-ce45-4ddd-afcc-9505641cff66/dqc_reference/checkm_data
[2024-01-24 10:48:04,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:04,980] [INFO] Task started: CheckM
[2024-01-24 10:48:04,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019710635.1_ASM1971063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019710635.1_ASM1971063v1_genomic.fna/checkm_input GCF_019710635.1_ASM1971063v1_genomic.fna/checkm_result
[2024-01-24 10:48:58,655] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:58,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:58,680] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:58,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:58,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019710635.1_ASM1971063v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:58,681] [INFO] Task started: Blastn
[2024-01-24 10:48:58,681] [INFO] Running command: blastn -query GCF_019710635.1_ASM1971063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1e6671d-ce45-4ddd-afcc-9505641cff66/dqc_reference/reference_markers_gtdb.fasta -out GCF_019710635.1_ASM1971063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:00,438] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:00,442] [INFO] Selected 20 target genomes.
[2024-01-24 10:49:00,443] [INFO] Target genome list was writen to GCF_019710635.1_ASM1971063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:00,458] [INFO] Task started: fastANI
[2024-01-24 10:49:00,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg174d575e-7573-420b-b461-bcb93049e72b/GCF_019710635.1_ASM1971063v1_genomic.fna.gz --refList GCF_019710635.1_ASM1971063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019710635.1_ASM1971063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:25,098] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:25,120] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:49:25,121] [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_001545925.1	s__Mycobacterium sp001545925	82.9062	948	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	82.6976	1157	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	82.6652	1127	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCA_000762985.1	s__Mycobacterium rufum_A	82.6265	1105	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017312405.1	s__Mycobacterium sp017312405	82.6116	1081	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_010728325.1	s__Mycobacterium poriferae	82.6084	1104	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.01	98.01	0.88	0.88	2	-
GCF_001044255.1	s__Mycobacterium chubuense	82.5679	1091	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_002086815.1	s__Mycobacterium parafortuitum	82.4055	1087	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010725485.1	s__Mycobacterium sp002946335	82.2469	1083	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.86	98.86	0.96	0.96	2	-
GCF_902705885.1	s__Mycobacterium vanbaalenii_A	82.0509	1105	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726645.1	s__Mycobacterium duvalii	81.9143	1023	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900454025.1	s__Mycobacterium gilvum	81.8885	1084	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_001583415.1	s__Mycobacterium phlei	81.7537	1019	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_007096635.1	s__Mycobacterium sp007096635	81.733	949	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500065.1	s__Mycobacterium sp001500065	80.6921	875	1793	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	80.184	652	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826815.1	s__Mycobacterium sp902826815	79.7996	867	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402475.1	s__Mycobacterium sp003402475	79.7883	734	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455125.1	s__Mycobacterium sp000455125	79.4213	640	1793	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_010723575.1	s__Mycobacterium bourgelatii	78.6559	652	1793	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 10:49:25,122] [INFO] GTDB search result was written to GCF_019710635.1_ASM1971063v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:25,123] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:25,130] [INFO] DFAST_QC result json was written to GCF_019710635.1_ASM1971063v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:25,130] [INFO] DFAST_QC completed!
[2024-01-24 10:49:25,131] [INFO] Total running time: 0h2m0s