[2024-01-25 19:24:45,021] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg8904818f-cc43-41c1-aa52-708a6ffad5ba/dqc_reference
[2024-01-25 19:24:48,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,895] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg29efe7c7-636e-4a45-8abe-c434b630ba6a/GCF_015710575.1_ASM1571057v2_genomic.fna.gz | prodigal -d GCF_015710575.1_ASM1571057v2_genomic.fna/cds.fna -a GCF_015710575.1_ASM1571057v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:25:06,223] [INFO] Task succeeded: Prodigal
[2024-01-25 19:25:06,223] [INFO] Task started: HMMsearch
[2024-01-25 19:25:06,223] [INFO] Running command: hmmsearch --tblout GCF_015710575.1_ASM1571057v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8904818f-cc43-41c1-aa52-708a6ffad5ba/dqc_reference/reference_markers.hmm GCF_015710575.1_ASM1571057v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:25:06,530] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:25:06,531] [INFO] Found 6/6 markers.
[2024-01-25 19:25:06,581] [INFO] Query marker FASTA was written to GCF_015710575.1_ASM1571057v2_genomic.fna/markers.fasta
[2024-01-25 19:25:06,581] [INFO] Task started: Blastn
[2024-01-25 19:25:06,581] [INFO] Running command: blastn -query GCF_015710575.1_ASM1571057v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8904818f-cc43-41c1-aa52-708a6ffad5ba/dqc_reference/reference_markers.fasta -out GCF_015710575.1_ASM1571057v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:07,789] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:07,791] [INFO] Selected 20 target genomes.
[2024-01-25 19:25:07,792] [INFO] Target genome list was writen to GCF_015710575.1_ASM1571057v2_genomic.fna/target_genomes.txt
[2024-01-25 19:25:08,182] [INFO] Task started: fastANI
[2024-01-25 19:25:08,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg29efe7c7-636e-4a45-8abe-c434b630ba6a/GCF_015710575.1_ASM1571057v2_genomic.fna.gz --refList GCF_015710575.1_ASM1571057v2_genomic.fna/target_genomes.txt --output GCF_015710575.1_ASM1571057v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:30,935] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:30,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8904818f-cc43-41c1-aa52-708a6ffad5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:30,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8904818f-cc43-41c1-aa52-708a6ffad5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:30,948] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:25:30,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:30,948] [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 mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	100.0	1986	1987	95	conclusive
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	81.3531	1115	1987	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	81.3077	1122	1987	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.1389	965	1987	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.0876	970	1987	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	80.0803	879	1987	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	79.9024	958	1987	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	79.8756	872	1987	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	79.867	878	1987	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	79.8458	874	1987	95	below_threshold
Mycolicibacterium confluentis	strain=DSM 44017	GCA_002102105.1	28047	28047	type	True	79.6887	887	1987	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	79.6568	911	1987	95	below_threshold
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	79.6501	911	1987	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5466	782	1987	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.4861	786	1987	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	79.1409	751	1987	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.1139	795	1987	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	79.0859	722	1987	95	below_threshold
Mycolicibacterium neoaurum	strain=ATCC 25795	GCA_000691525.1	1795	1795	type	True	79.0712	725	1987	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	78.758	645	1987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:30,951] [INFO] DFAST Taxonomy check result was written to GCF_015710575.1_ASM1571057v2_genomic.fna/tc_result.tsv
[2024-01-25 19:25:30,951] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:30,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:30,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8904818f-cc43-41c1-aa52-708a6ffad5ba/dqc_reference/checkm_data
[2024-01-25 19:25:30,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:31,009] [INFO] Task started: CheckM
[2024-01-25 19:25:31,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015710575.1_ASM1571057v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015710575.1_ASM1571057v2_genomic.fna/checkm_input GCF_015710575.1_ASM1571057v2_genomic.fna/checkm_result
[2024-01-25 19:26:37,707] [INFO] Task succeeded: CheckM
[2024-01-25 19:26:37,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:26:37,734] [INFO] ===== Completeness check finished =====
[2024-01-25 19:26:37,734] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:26:37,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015710575.1_ASM1571057v2_genomic.fna/markers.fasta)
[2024-01-25 19:26:37,736] [INFO] Task started: Blastn
[2024-01-25 19:26:37,736] [INFO] Running command: blastn -query GCF_015710575.1_ASM1571057v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8904818f-cc43-41c1-aa52-708a6ffad5ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_015710575.1_ASM1571057v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:26:39,725] [INFO] Task succeeded: Blastn
[2024-01-25 19:26:39,728] [INFO] Selected 21 target genomes.
[2024-01-25 19:26:39,728] [INFO] Target genome list was writen to GCF_015710575.1_ASM1571057v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:26:39,767] [INFO] Task started: fastANI
[2024-01-25 19:26:39,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg29efe7c7-636e-4a45-8abe-c434b630ba6a/GCF_015710575.1_ASM1571057v2_genomic.fna.gz --refList GCF_015710575.1_ASM1571057v2_genomic.fna/target_genomes_gtdb.txt --output GCF_015710575.1_ASM1571057v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:27:05,653] [INFO] Task succeeded: fastANI
[2024-01-25 19:27:05,665] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:27:05,665] [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_015710575.1	s__Mycobacterium sp015710575	100.0	1986	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	99.09	0.96	0.96	2	conclusive
GCF_010725885.1	s__Mycobacterium tokaiense	81.3296	1118	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	96.52	0.94	0.90	4	-
GCF_001984215.1	s__Mycobacterium sp001984215	81.1732	1107	1987	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	80.1336	966	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_001552715.1	s__Mycobacterium vaccae	80.0479	885	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_001583415.1	s__Mycobacterium phlei	79.8762	877	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900078775.1	s__Mycobacterium aurum_A	79.8267	871	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	79.8165	780	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667265.1	s__Mycobacterium sp001667265	79.7309	865	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218295.1	s__Mycobacterium litorale_B	79.7252	932	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	79.7032	880	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729895.1	s__Mycobacterium confluentis	79.6559	910	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001500125.1	s__Mycobacterium sp001500125	79.5264	852	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002007745.1	s__Mycobacterium litorale_A	79.5161	794	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011694515.1	s__Mycobacterium sp011694515	79.5104	778	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230935.1	s__Mycobacterium rhodesiae_B	79.2458	807	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	79.1606	810	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_002250655.1	s__Mycobacterium sphagni	79.144	751	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005670685.2	s__Mycobacterium mucogenicum_B	79.1409	716	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.72	96.94	0.94	0.86	7	-
GCF_014202335.1	s__Mycobacterium sp014202335	78.9584	833	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731595.1	s__Mycobacterium seoulense	78.764	644	1987	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 19:27:05,667] [INFO] GTDB search result was written to GCF_015710575.1_ASM1571057v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:27:05,667] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:27:05,674] [INFO] DFAST_QC result json was written to GCF_015710575.1_ASM1571057v2_genomic.fna/dqc_result.json
[2024-01-25 19:27:05,674] [INFO] DFAST_QC completed!
[2024-01-25 19:27:05,674] [INFO] Total running time: 0h2m21s