[2023-03-15 14:23:02,725] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:23:02,733] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:23:02,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg993e28c6-e2f6-4538-82a3-95b96afdc6df/dqc_reference
[2023-03-15 14:23:03,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:23:03,859] [INFO] Task started: Prodigal
[2023-03-15 14:23:03,859] [INFO] Running command: cat /var/lib/cwl/stg654b893c-b1fb-4abc-a2e8-303ddbeabd8e/OceanDNA-b43.fa | prodigal -d OceanDNA-b43/cds.fna -a OceanDNA-b43/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:23:59,072] [INFO] Task succeeded: Prodigal
[2023-03-15 14:23:59,073] [INFO] Task started: HMMsearch
[2023-03-15 14:23:59,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b43/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg993e28c6-e2f6-4538-82a3-95b96afdc6df/dqc_reference/reference_markers.hmm OceanDNA-b43/protein.faa > /dev/null
[2023-03-15 14:23:59,383] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:23:59,384] [INFO] Found 6/6 markers.
[2023-03-15 14:23:59,532] [INFO] Query marker FASTA was written to OceanDNA-b43/markers.fasta
[2023-03-15 14:23:59,534] [INFO] Task started: Blastn
[2023-03-15 14:23:59,534] [INFO] Running command: blastn -query OceanDNA-b43/markers.fasta -db /var/lib/cwl/stg993e28c6-e2f6-4538-82a3-95b96afdc6df/dqc_reference/reference_markers.fasta -out OceanDNA-b43/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:24:00,123] [INFO] Task succeeded: Blastn
[2023-03-15 14:24:00,166] [INFO] Selected 40 target genomes.
[2023-03-15 14:24:00,166] [INFO] Target genome list was writen to OceanDNA-b43/target_genomes.txt
[2023-03-15 14:24:00,199] [INFO] Task started: fastANI
[2023-03-15 14:24:00,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg654b893c-b1fb-4abc-a2e8-303ddbeabd8e/OceanDNA-b43.fa --refList OceanDNA-b43/target_genomes.txt --output OceanDNA-b43/fastani_result.tsv --threads 1
[2023-03-15 14:24:27,439] [INFO] Task succeeded: fastANI
[2023-03-15 14:24:27,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg993e28c6-e2f6-4538-82a3-95b96afdc6df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:24:27,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg993e28c6-e2f6-4538-82a3-95b96afdc6df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:24:27,455] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:24:27,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:24:27,455] [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
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	74.9504	103	2665	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	74.942	63	2665	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	74.9297	58	2665	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	74.9254	81	2665	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	74.9224	53	2665	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	74.8851	78	2665	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	74.8562	82	2665	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	74.8444	58	2665	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	74.8324	87	2665	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	74.8097	74	2665	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	74.7686	84	2665	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	74.7631	90	2665	95	below_threshold
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	74.7525	91	2665	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	74.7451	62	2665	95	below_threshold
Streptomyces purpurogeneiscleroticus	strain=DSM 43156	GCA_020024005.1	68259	68259	type	True	74.7328	144	2665	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	74.7242	76	2665	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	74.7178	71	2665	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	74.715	92	2665	95	below_threshold
Streptomyces bohaiensis	strain=11A07	GCA_012033785.1	1431344	1431344	type	True	74.6977	94	2665	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	74.6938	114	2665	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	74.679	77	2665	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	74.6765	80	2665	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	74.6755	79	2665	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	74.6751	54	2665	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	74.6728	61	2665	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	74.6111	182	2665	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	74.6083	103	2665	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	74.6083	103	2665	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	74.5966	184	2665	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:24:27,472] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43/tc_result.tsv
[2023-03-15 14:24:27,500] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:24:27,501] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:24:27,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg993e28c6-e2f6-4538-82a3-95b96afdc6df/dqc_reference/checkm_data
[2023-03-15 14:24:27,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:24:27,550] [INFO] Task started: CheckM
[2023-03-15 14:24:27,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43/checkm_input OceanDNA-b43/checkm_result
[2023-03-15 14:26:37,337] [INFO] Task succeeded: CheckM
[2023-03-15 14:26:37,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:26:37,342] [INFO] ===== Completeness check finished =====
[2023-03-15 14:26:37,342] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:26:37,342] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43/markers.fasta)
[2023-03-15 14:26:37,343] [INFO] Task started: Blastn
[2023-03-15 14:26:37,343] [INFO] Running command: blastn -query OceanDNA-b43/markers.fasta -db /var/lib/cwl/stg993e28c6-e2f6-4538-82a3-95b96afdc6df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:26:38,235] [INFO] Task succeeded: Blastn
[2023-03-15 14:26:38,236] [INFO] Selected 39 target genomes.
[2023-03-15 14:26:38,236] [INFO] Target genome list was writen to OceanDNA-b43/target_genomes_gtdb.txt
[2023-03-15 14:26:38,377] [INFO] Task started: fastANI
[2023-03-15 14:26:38,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg654b893c-b1fb-4abc-a2e8-303ddbeabd8e/OceanDNA-b43.fa --refList OceanDNA-b43/target_genomes_gtdb.txt --output OceanDNA-b43/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:27:03,780] [INFO] Task succeeded: fastANI
[2023-03-15 14:27:03,793] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:27:03,794] [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_003697015.1	s__J023 sp003697015	76.105	376	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003231035.1	s__SZUA-115 sp003231035	75.5894	97	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__SZUA-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009836625.1	s__WTGL01 sp009836625	75.3815	115	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.03	98.03	0.95	0.91	5	-
GCA_009843505.1	s__WTGL01 sp009843505	75.3496	117	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_003388555.1	s__QQVD01 sp003388555	75.3336	233	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_011525905.1	s__JACTMI01 sp011525905	75.2687	151	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525365.1	s__WTGL01 sp011525365	75.2642	106	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837085.1	s__WTGL01 sp009837085	75.2502	118	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_017998715.1	s__JAGPDF01 sp017998715	75.233	124	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420005.1	s__UBA5704 sp002420005	75.2027	226	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270995.1	s__WTGL01 sp012270995	75.1755	117	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.1737	168	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227875.1	s__M0029 sp006227875	75.1019	67	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__M0029	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152925.1	s__JAADFK01 sp013152925	75.0864	69	2665	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__FEB-10;g__JAADFK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	74.9254	81	2665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.94	98.42	0.92	0.89	3	-
GCA_003242275.1	s__ZC4RG30 sp003242275	74.9104	65	2665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422205.1	s__Desulfohalovibrio sp000422205	74.8122	94	2665	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfohalovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	74.8015	64	2665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268715.1	s__TMP-7 sp018268715	74.7579	90	2665	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__TMP-7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	74.7451	62	2665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCA_016713665.1	s__JADJOR01 sp016713665	74.7337	134	2665	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	74.7026	70	2665	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693815.1	s__Arachnia lapidicapta	74.6728	61	2665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.86	97.76	0.95	0.93	4	-
GCF_000295855.1	s__Mycobacterium fortuitum	74.6716	80	2665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCA_017302815.1	s__UBA11346 sp017302815	74.6414	75	2665	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__UBA11346	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:27:03,794] [INFO] GTDB search result was written to OceanDNA-b43/result_gtdb.tsv
[2023-03-15 14:27:03,794] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:27:03,797] [INFO] DFAST_QC result json was written to OceanDNA-b43/dqc_result.json
[2023-03-15 14:27:03,797] [INFO] DFAST_QC completed!
[2023-03-15 14:27:03,797] [INFO] Total running time: 0h4m1s