[2023-06-08 01:21:19,666] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:21:19,669] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:21:19,669] [INFO] DQC Reference Directory: /var/lib/cwl/stgad82e0bf-bdc4-4b8e-a53a-e10d7b255cbb/dqc_reference
[2023-06-08 01:21:21,168] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:21:21,169] [INFO] Task started: Prodigal
[2023-06-08 01:21:21,170] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c1bf3d3-3f07-4294-baba-d22b1e87e3ca/GCA_945871255.1_MsE-30apr19-112_genomic.fna.gz | prodigal -d GCA_945871255.1_MsE-30apr19-112_genomic.fna/cds.fna -a GCA_945871255.1_MsE-30apr19-112_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:21:28,987] [INFO] Task succeeded: Prodigal
[2023-06-08 01:21:28,988] [INFO] Task started: HMMsearch
[2023-06-08 01:21:28,988] [INFO] Running command: hmmsearch --tblout GCA_945871255.1_MsE-30apr19-112_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad82e0bf-bdc4-4b8e-a53a-e10d7b255cbb/dqc_reference/reference_markers.hmm GCA_945871255.1_MsE-30apr19-112_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:21:29,223] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:21:29,225] [INFO] Found 6/6 markers.
[2023-06-08 01:21:29,253] [INFO] Query marker FASTA was written to GCA_945871255.1_MsE-30apr19-112_genomic.fna/markers.fasta
[2023-06-08 01:21:29,253] [INFO] Task started: Blastn
[2023-06-08 01:21:29,254] [INFO] Running command: blastn -query GCA_945871255.1_MsE-30apr19-112_genomic.fna/markers.fasta -db /var/lib/cwl/stgad82e0bf-bdc4-4b8e-a53a-e10d7b255cbb/dqc_reference/reference_markers.fasta -out GCA_945871255.1_MsE-30apr19-112_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:21:30,344] [INFO] Task succeeded: Blastn
[2023-06-08 01:21:30,349] [INFO] Selected 28 target genomes.
[2023-06-08 01:21:30,350] [INFO] Target genome list was writen to GCA_945871255.1_MsE-30apr19-112_genomic.fna/target_genomes.txt
[2023-06-08 01:21:30,357] [INFO] Task started: fastANI
[2023-06-08 01:21:30,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c1bf3d3-3f07-4294-baba-d22b1e87e3ca/GCA_945871255.1_MsE-30apr19-112_genomic.fna.gz --refList GCA_945871255.1_MsE-30apr19-112_genomic.fna/target_genomes.txt --output GCA_945871255.1_MsE-30apr19-112_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:21:53,073] [INFO] Task succeeded: fastANI
[2023-06-08 01:21:53,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad82e0bf-bdc4-4b8e-a53a-e10d7b255cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:21:53,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad82e0bf-bdc4-4b8e-a53a-e10d7b255cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:21:53,107] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:21:53,107] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 01:21:53,107] [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
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.6173	437	839	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.3519	517	839	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	78.9796	475	839	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	78.9498	495	839	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	78.867	496	839	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	78.8637	343	839	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	78.8376	413	839	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	78.8093	494	839	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	78.7908	417	839	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	78.7803	488	839	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	78.7526	358	839	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	78.7132	429	839	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	78.6807	423	839	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	78.6283	479	839	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	78.5994	442	839	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	78.4977	393	839	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	78.4837	353	839	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	78.4762	405	839	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	78.4581	408	839	95	below_threshold
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	78.4476	397	839	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	78.397	403	839	95	below_threshold
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	78.3563	413	839	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	78.2924	339	839	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	78.2752	381	839	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	78.1619	384	839	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	78.1556	389	839	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	78.0935	359	839	95	below_threshold
Mycolicibacterium neoaurum	strain=ATCC 25795	GCA_000691525.1	1795	1795	type	True	78.0495	356	839	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:21:53,110] [INFO] DFAST Taxonomy check result was written to GCA_945871255.1_MsE-30apr19-112_genomic.fna/tc_result.tsv
[2023-06-08 01:21:53,111] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:21:53,111] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:21:53,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad82e0bf-bdc4-4b8e-a53a-e10d7b255cbb/dqc_reference/checkm_data
[2023-06-08 01:21:53,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:21:53,145] [INFO] Task started: CheckM
[2023-06-08 01:21:53,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945871255.1_MsE-30apr19-112_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945871255.1_MsE-30apr19-112_genomic.fna/checkm_input GCA_945871255.1_MsE-30apr19-112_genomic.fna/checkm_result
[2023-06-08 01:22:20,559] [INFO] Task succeeded: CheckM
[2023-06-08 01:22:20,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:22:20,583] [INFO] ===== Completeness check finished =====
[2023-06-08 01:22:20,583] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:22:20,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945871255.1_MsE-30apr19-112_genomic.fna/markers.fasta)
[2023-06-08 01:22:20,584] [INFO] Task started: Blastn
[2023-06-08 01:22:20,584] [INFO] Running command: blastn -query GCA_945871255.1_MsE-30apr19-112_genomic.fna/markers.fasta -db /var/lib/cwl/stgad82e0bf-bdc4-4b8e-a53a-e10d7b255cbb/dqc_reference/reference_markers_gtdb.fasta -out GCA_945871255.1_MsE-30apr19-112_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:22:22,173] [INFO] Task succeeded: Blastn
[2023-06-08 01:22:22,177] [INFO] Selected 17 target genomes.
[2023-06-08 01:22:22,177] [INFO] Target genome list was writen to GCA_945871255.1_MsE-30apr19-112_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:22:22,211] [INFO] Task started: fastANI
[2023-06-08 01:22:22,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c1bf3d3-3f07-4294-baba-d22b1e87e3ca/GCA_945871255.1_MsE-30apr19-112_genomic.fna.gz --refList GCA_945871255.1_MsE-30apr19-112_genomic.fna/target_genomes_gtdb.txt --output GCA_945871255.1_MsE-30apr19-112_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:22:35,144] [INFO] Task succeeded: fastANI
[2023-06-08 01:22:35,165] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:22:35,165] [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
GCA_903911165.1	s__Mycobacterium sp903911165	98.3868	640	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005789055.1	s__Mycobacterium sp005789055	90.5965	411	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401645.1	s__Mycobacterium sp018401645	83.051	587	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462945.1	s__Mycobacterium sp016462945	82.0582	612	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853185.1	s__Mycobacterium sp017853185	80.0812	504	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884065.1	s__Mycobacterium sp903884065	79.9478	564	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
GCA_001510415.1	s__Mycobacterium sp001510415	79.8254	311	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877095.1	s__Mycobacterium sp903877095	79.6528	520	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.96	99.94	0.97	0.96	4	-
GCF_010731855.1	s__Mycobacterium anyangense	79.3611	516	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787665.1	s__Mycobacterium sp005787665	79.316	399	839	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	78.9091	505	839	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	78.8797	526	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	78.577	407	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018455725.1	s__Mycobacterium sp018455725	78.4684	371	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	78.4472	408	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCA_900637135.1	s__Mycobacterium flavescens	78.2769	355	839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-08 01:22:35,168] [INFO] GTDB search result was written to GCA_945871255.1_MsE-30apr19-112_genomic.fna/result_gtdb.tsv
[2023-06-08 01:22:35,168] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:22:35,173] [INFO] DFAST_QC result json was written to GCA_945871255.1_MsE-30apr19-112_genomic.fna/dqc_result.json
[2023-06-08 01:22:35,173] [INFO] DFAST_QC completed!
[2023-06-08 01:22:35,173] [INFO] Total running time: 0h1m16s