[2024-01-25 18:51:50,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8abb5e7-a11d-4c44-97f4-c7964258ee77/dqc_reference
[2024-01-25 18:51:51,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,712] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,712] [INFO] Running command: gunzip -c /var/lib/cwl/stgec881b32-15a2-4906-b09b-e4db7ae66bcb/GCF_025823005.1_ASM2582300v1_genomic.fna.gz | prodigal -d GCF_025823005.1_ASM2582300v1_genomic.fna/cds.fna -a GCF_025823005.1_ASM2582300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:08,739] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:08,739] [INFO] Task started: HMMsearch
[2024-01-25 18:52:08,739] [INFO] Running command: hmmsearch --tblout GCF_025823005.1_ASM2582300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8abb5e7-a11d-4c44-97f4-c7964258ee77/dqc_reference/reference_markers.hmm GCF_025823005.1_ASM2582300v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:09,028] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:09,029] [INFO] Found 6/6 markers.
[2024-01-25 18:52:09,076] [INFO] Query marker FASTA was written to GCF_025823005.1_ASM2582300v1_genomic.fna/markers.fasta
[2024-01-25 18:52:09,077] [INFO] Task started: Blastn
[2024-01-25 18:52:09,077] [INFO] Running command: blastn -query GCF_025823005.1_ASM2582300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8abb5e7-a11d-4c44-97f4-c7964258ee77/dqc_reference/reference_markers.fasta -out GCF_025823005.1_ASM2582300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:10,294] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:10,297] [INFO] Selected 26 target genomes.
[2024-01-25 18:52:10,297] [INFO] Target genome list was writen to GCF_025823005.1_ASM2582300v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:10,350] [INFO] Task started: fastANI
[2024-01-25 18:52:10,350] [INFO] Running command: fastANI --query /var/lib/cwl/stgec881b32-15a2-4906-b09b-e4db7ae66bcb/GCF_025823005.1_ASM2582300v1_genomic.fna.gz --refList GCF_025823005.1_ASM2582300v1_genomic.fna/target_genomes.txt --output GCF_025823005.1_ASM2582300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:39,877] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:39,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8abb5e7-a11d-4c44-97f4-c7964258ee77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:39,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8abb5e7-a11d-4c44-97f4-c7964258ee77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:39,892] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:52:39,893] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:52:39,893] [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 vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	82.422	1074	1853	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	82.3715	1167	1853	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	81.9931	1100	1853	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	81.9859	1117	1853	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	81.9392	1097	1853	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	81.893	1117	1853	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.3687	1054	1853	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.3544	1057	1853	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.3527	1056	1853	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.1686	1056	1853	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.0466	1096	1853	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.0064	1103	1853	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.5614	979	1853	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.3789	940	1853	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.343	941	1853	95	below_threshold
Mycobacterium doricum	strain=JCM 12405	GCA_010728155.1	126673	126673	type	True	80.2697	710	1853	95	below_threshold
Mycobacterium doricum	strain=DSM 44339	GCA_002102115.1	126673	126673	type	True	80.2515	690	1853	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	79.924	927	1853	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	79.8779	918	1853	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	79.8188	917	1853	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.7768	896	1853	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.751	845	1853	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.6939	895	1853	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6074	832	1853	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5891	833	1853	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.4629	794	1853	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:39,894] [INFO] DFAST Taxonomy check result was written to GCF_025823005.1_ASM2582300v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:39,895] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:39,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:39,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8abb5e7-a11d-4c44-97f4-c7964258ee77/dqc_reference/checkm_data
[2024-01-25 18:52:39,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:39,948] [INFO] Task started: CheckM
[2024-01-25 18:52:39,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823005.1_ASM2582300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823005.1_ASM2582300v1_genomic.fna/checkm_input GCF_025823005.1_ASM2582300v1_genomic.fna/checkm_result
[2024-01-25 18:53:40,392] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:40,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:40,412] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:40,412] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:40,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823005.1_ASM2582300v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:40,413] [INFO] Task started: Blastn
[2024-01-25 18:53:40,413] [INFO] Running command: blastn -query GCF_025823005.1_ASM2582300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8abb5e7-a11d-4c44-97f4-c7964258ee77/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823005.1_ASM2582300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:42,428] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:42,431] [INFO] Selected 21 target genomes.
[2024-01-25 18:53:42,431] [INFO] Target genome list was writen to GCF_025823005.1_ASM2582300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:42,450] [INFO] Task started: fastANI
[2024-01-25 18:53:42,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgec881b32-15a2-4906-b09b-e4db7ae66bcb/GCF_025823005.1_ASM2582300v1_genomic.fna.gz --refList GCF_025823005.1_ASM2582300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823005.1_ASM2582300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:09,349] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:09,362] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:09,362] [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_010726645.1	s__Mycobacterium duvalii	99.994	1851	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001545925.1	s__Mycobacterium sp001545925	82.6176	981	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	82.3996	1078	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_900454025.1	s__Mycobacterium gilvum	82.3043	1214	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_001722335.1	s__Mycobacterium flavescens_A	82.1646	1093	1853	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	82.1076	1165	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_002086815.1	s__Mycobacterium parafortuitum	82.0782	1155	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	81.9492	1129	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725485.1	s__Mycobacterium sp002946335	81.9216	1184	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.86	98.86	0.96	0.96	2	-
GCF_000266905.1	s__Mycobacterium chubuense_A	81.7485	1164	1853	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	81.3426	1058	1853	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	81.2358	960	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108565.1	s__Mycobacterium rutilum	81.1863	1054	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637195.1	s__Mycobacterium aurum	81.0489	1096	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001500125.1	s__Mycobacterium sp001500125	80.7465	985	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050015.1	s__Mycobacterium malmesburyense	80.5432	983	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500025.1	s__Mycobacterium sp001500025	80.3955	950	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016313185.1	s__Mycobacterium sp016313185	80.3603	939	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_010728155.1	s__Mycobacterium doricum	80.2614	711	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900637135.1	s__Mycobacterium flavescens	80.2115	945	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001499905.1	s__Mycobacterium sp001499905	80.1441	910	1853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:09,363] [INFO] GTDB search result was written to GCF_025823005.1_ASM2582300v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:09,364] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:09,367] [INFO] DFAST_QC result json was written to GCF_025823005.1_ASM2582300v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:09,368] [INFO] DFAST_QC completed!
[2024-01-25 18:54:09,368] [INFO] Total running time: 0h2m19s