[2024-01-25 17:34:07,124] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,128] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeed21c6-05aa-4087-8cc6-e88e474905be/dqc_reference
[2024-01-25 17:34:09,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,030] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,030] [INFO] Running command: gunzip -c /var/lib/cwl/stgbed9bc95-13a9-44ac-9e05-724180faaf9e/GCF_025822845.1_ASM2582284v1_genomic.fna.gz | prodigal -d GCF_025822845.1_ASM2582284v1_genomic.fna/cds.fna -a GCF_025822845.1_ASM2582284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:27,084] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:27,084] [INFO] Task started: HMMsearch
[2024-01-25 17:34:27,084] [INFO] Running command: hmmsearch --tblout GCF_025822845.1_ASM2582284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeed21c6-05aa-4087-8cc6-e88e474905be/dqc_reference/reference_markers.hmm GCF_025822845.1_ASM2582284v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:27,411] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:27,412] [INFO] Found 6/6 markers.
[2024-01-25 17:34:27,459] [INFO] Query marker FASTA was written to GCF_025822845.1_ASM2582284v1_genomic.fna/markers.fasta
[2024-01-25 17:34:27,459] [INFO] Task started: Blastn
[2024-01-25 17:34:27,459] [INFO] Running command: blastn -query GCF_025822845.1_ASM2582284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeed21c6-05aa-4087-8cc6-e88e474905be/dqc_reference/reference_markers.fasta -out GCF_025822845.1_ASM2582284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:28,800] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:28,803] [INFO] Selected 24 target genomes.
[2024-01-25 17:34:28,804] [INFO] Target genome list was writen to GCF_025822845.1_ASM2582284v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:28,811] [INFO] Task started: fastANI
[2024-01-25 17:34:28,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed9bc95-13a9-44ac-9e05-724180faaf9e/GCF_025822845.1_ASM2582284v1_genomic.fna.gz --refList GCF_025822845.1_ASM2582284v1_genomic.fna/target_genomes.txt --output GCF_025822845.1_ASM2582284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:57,677] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:57,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeed21c6-05aa-4087-8cc6-e88e474905be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:57,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeed21c6-05aa-4087-8cc6-e88e474905be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:57,691] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:57,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:57,691] [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 confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	99.9944	1927	1932	95	conclusive
Mycolicibacterium confluentis	strain=DSM 44017	GCA_002102105.1	28047	28047	type	True	99.9882	1904	1932	95	conclusive
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	82.0122	1140	1932	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	81.9791	1129	1932	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.672	963	1932	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.5766	973	1932	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	80.2853	946	1932	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.1129	911	1932	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	80.0439	895	1932	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	80.0412	682	1932	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.0412	917	1932	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	79.9874	672	1932	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	79.8359	937	1932	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	79.823	899	1932	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.7217	880	1932	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.7029	859	1932	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.6595	885	1932	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	79.633	843	1932	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.623	856	1932	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.5033	848	1932	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	79.4942	890	1932	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.4713	879	1932	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	79.003	724	1932	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	78.8588	828	1932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:57,693] [INFO] DFAST Taxonomy check result was written to GCF_025822845.1_ASM2582284v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:57,694] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:57,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:57,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeed21c6-05aa-4087-8cc6-e88e474905be/dqc_reference/checkm_data
[2024-01-25 17:34:57,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:57,749] [INFO] Task started: CheckM
[2024-01-25 17:34:57,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822845.1_ASM2582284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822845.1_ASM2582284v1_genomic.fna/checkm_input GCF_025822845.1_ASM2582284v1_genomic.fna/checkm_result
[2024-01-25 17:36:22,584] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:22,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:22,604] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:22,604] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:22,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822845.1_ASM2582284v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:22,606] [INFO] Task started: Blastn
[2024-01-25 17:36:22,606] [INFO] Running command: blastn -query GCF_025822845.1_ASM2582284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeed21c6-05aa-4087-8cc6-e88e474905be/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822845.1_ASM2582284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:24,745] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:24,748] [INFO] Selected 20 target genomes.
[2024-01-25 17:36:24,749] [INFO] Target genome list was writen to GCF_025822845.1_ASM2582284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:24,758] [INFO] Task started: fastANI
[2024-01-25 17:36:24,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed9bc95-13a9-44ac-9e05-724180faaf9e/GCF_025822845.1_ASM2582284v1_genomic.fna.gz --refList GCF_025822845.1_ASM2582284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822845.1_ASM2582284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:50,036] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:50,049] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:50,049] [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_010729895.1	s__Mycobacterium confluentis	99.9944	1927	1932	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_001667265.1	s__Mycobacterium sp001667265	90.1132	1600	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637205.1	s__Mycobacterium chitae	81.9656	1132	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001583415.1	s__Mycobacterium phlei	80.6963	959	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_002592005.1	s__Mycobacterium palauense	80.5605	976	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078775.1	s__Mycobacterium aurum_A	80.4675	1016	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	80.444	1011	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_001457595.1	s__Mycobacterium smegmatis	80.3833	1037	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.2301	820	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014795.1	s__Mycobacterium brumae	79.9942	671	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.98	0.98	0.98	3	-
GCF_004570325.1	s__Mycobacterium sp004570325	79.9668	896	1932	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	79.9578	967	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_002798385.1	s__Mycobacterium goodii	79.9448	928	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_005670685.2	s__Mycobacterium mucogenicum_B	79.782	801	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.72	96.94	0.94	0.86	7	-
GCF_002086835.1	s__Mycobacterium porcinum	79.7519	934	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_009729095.1	s__Mycobacterium sp009729095	79.7189	905	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_015710575.1	s__Mycobacterium sp015710575	79.718	881	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	99.09	0.96	0.96	2	-
GCF_004014805.1	s__Mycobacterium elephantis	79.6531	841	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_016313185.1	s__Mycobacterium sp016313185	79.5232	885	1932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCA_017853185.1	s__Mycobacterium sp017853185	79.4786	549	1932	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 17:36:50,051] [INFO] GTDB search result was written to GCF_025822845.1_ASM2582284v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:50,052] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:50,056] [INFO] DFAST_QC result json was written to GCF_025822845.1_ASM2582284v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:50,056] [INFO] DFAST_QC completed!
[2024-01-25 17:36:50,056] [INFO] Total running time: 0h2m43s