[2024-01-25 19:53:35,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c6d8426-ae63-4558-96b1-e4771337179e/dqc_reference
[2024-01-25 19:53:36,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,763] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5c3d849-457c-4b16-8d08-c5c08d67790e/GCF_025822165.1_ASM2582216v1_genomic.fna.gz | prodigal -d GCF_025822165.1_ASM2582216v1_genomic.fna/cds.fna -a GCF_025822165.1_ASM2582216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:54,892] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:54,892] [INFO] Task started: HMMsearch
[2024-01-25 19:53:54,893] [INFO] Running command: hmmsearch --tblout GCF_025822165.1_ASM2582216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c6d8426-ae63-4558-96b1-e4771337179e/dqc_reference/reference_markers.hmm GCF_025822165.1_ASM2582216v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:55,175] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:55,176] [INFO] Found 6/6 markers.
[2024-01-25 19:53:55,223] [INFO] Query marker FASTA was written to GCF_025822165.1_ASM2582216v1_genomic.fna/markers.fasta
[2024-01-25 19:53:55,224] [INFO] Task started: Blastn
[2024-01-25 19:53:55,224] [INFO] Running command: blastn -query GCF_025822165.1_ASM2582216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6d8426-ae63-4558-96b1-e4771337179e/dqc_reference/reference_markers.fasta -out GCF_025822165.1_ASM2582216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:56,344] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:56,346] [INFO] Selected 24 target genomes.
[2024-01-25 19:53:56,347] [INFO] Target genome list was writen to GCF_025822165.1_ASM2582216v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:56,354] [INFO] Task started: fastANI
[2024-01-25 19:53:56,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c3d849-457c-4b16-8d08-c5c08d67790e/GCF_025822165.1_ASM2582216v1_genomic.fna.gz --refList GCF_025822165.1_ASM2582216v1_genomic.fna/target_genomes.txt --output GCF_025822165.1_ASM2582216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:23,263] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:23,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c6d8426-ae63-4558-96b1-e4771337179e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:23,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c6d8426-ae63-4558-96b1-e4771337179e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:23,278] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:54:23,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:54:23,279] [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
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	91.3335	1496	2032	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	90.7834	1492	2032	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	88.1703	1416	2032	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	87.6721	1433	2032	95	below_threshold
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	84.7844	1259	2032	95	below_threshold
Mycolicibacterium celeriflavum	strain=JCM 18439	GCA_010731795.1	1249101	1249101	type	True	84.7344	1275	2032	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	84.2396	1318	2032	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.9678	1181	2032	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	82.8936	1207	2032	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.2969	917	2032	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	80.2608	893	2032	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	80.057	915	2032	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.9072	915	2032	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.7555	864	2032	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	79.6488	693	2032	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.6397	848	2032	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	79.598	714	2032	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.5516	757	2032	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.0916	734	2032	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	77.5685	464	2032	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	77.5223	468	2032	95	below_threshold
Rhodococcus phenolicus	strain=DSM 44812	GCA_001646785.1	263849	263849	type	True	77.51	437	2032	95	below_threshold
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	77.4789	447	2032	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	77.4126	455	2032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:23,280] [INFO] DFAST Taxonomy check result was written to GCF_025822165.1_ASM2582216v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:23,281] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:23,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:23,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c6d8426-ae63-4558-96b1-e4771337179e/dqc_reference/checkm_data
[2024-01-25 19:54:23,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:23,339] [INFO] Task started: CheckM
[2024-01-25 19:54:23,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822165.1_ASM2582216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822165.1_ASM2582216v1_genomic.fna/checkm_input GCF_025822165.1_ASM2582216v1_genomic.fna/checkm_result
[2024-01-25 19:55:23,845] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:23,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:23,861] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:23,862] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:23,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822165.1_ASM2582216v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:23,862] [INFO] Task started: Blastn
[2024-01-25 19:55:23,862] [INFO] Running command: blastn -query GCF_025822165.1_ASM2582216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6d8426-ae63-4558-96b1-e4771337179e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822165.1_ASM2582216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:25,576] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:25,579] [INFO] Selected 19 target genomes.
[2024-01-25 19:55:25,579] [INFO] Target genome list was writen to GCF_025822165.1_ASM2582216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:25,588] [INFO] Task started: fastANI
[2024-01-25 19:55:25,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c3d849-457c-4b16-8d08-c5c08d67790e/GCF_025822165.1_ASM2582216v1_genomic.fna.gz --refList GCF_025822165.1_ASM2582216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822165.1_ASM2582216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:50,386] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:50,398] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:50,398] [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_001570485.1	s__Mycobacterium novocastrense	99.9878	2001	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	conclusive
GCF_001500025.1	s__Mycobacterium sp001500025	92.2851	1580	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245535.1	s__Mycobacterium lehmannii	91.3352	1496	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCA_900637135.1	s__Mycobacterium flavescens	90.765	1515	2032	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	89.5578	1395	2032	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	88.1539	1418	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665535.1	s__Mycobacterium sp001665535	87.5559	1465	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001668575.1	s__Mycobacterium sp001668575	87.2587	1443	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284965.1	s__Mycobacterium sp003284965	85.5331	1392	2032	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	84.5722	1293	2032	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	83.9526	1320	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722355.1	s__Mycobacterium holsaticum	81.9143	1065	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347205.1	s__Mycobacterium moriokaense_B	81.6006	1059	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002592005.1	s__Mycobacterium palauense	79.9982	872	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	79.7479	927	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCF_001668625.1	s__Mycobacterium sp001668625	79.5678	630	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058165.1	s__Rhodococcus aetherivorans	77.5645	464	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_001646785.1	s__Rhodococcus phenolicus	77.5171	436	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250675.2	s__Nocardia brasiliensis_B	77.4076	471	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:50,411] [INFO] GTDB search result was written to GCF_025822165.1_ASM2582216v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:50,412] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:50,416] [INFO] DFAST_QC result json was written to GCF_025822165.1_ASM2582216v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:50,416] [INFO] DFAST_QC completed!
[2024-01-25 19:55:50,416] [INFO] Total running time: 0h2m15s