[2023-06-13 13:31:54,127] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:31:54,132] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:31:54,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg1389d4ca-b007-4ce0-86a6-336b393d7886/dqc_reference
[2023-06-13 13:31:55,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:31:55,554] [INFO] Task started: Prodigal
[2023-06-13 13:31:55,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg459d008a-4663-44ee-a2aa-13c98ce5482d/GCA_947475545.1_RH-23may17-645_genomic.fna.gz | prodigal -d GCA_947475545.1_RH-23may17-645_genomic.fna/cds.fna -a GCA_947475545.1_RH-23may17-645_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:32:04,994] [INFO] Task succeeded: Prodigal
[2023-06-13 13:32:04,994] [INFO] Task started: HMMsearch
[2023-06-13 13:32:04,994] [INFO] Running command: hmmsearch --tblout GCA_947475545.1_RH-23may17-645_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1389d4ca-b007-4ce0-86a6-336b393d7886/dqc_reference/reference_markers.hmm GCA_947475545.1_RH-23may17-645_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:32:05,300] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:32:05,302] [INFO] Found 6/6 markers.
[2023-06-13 13:32:05,334] [INFO] Query marker FASTA was written to GCA_947475545.1_RH-23may17-645_genomic.fna/markers.fasta
[2023-06-13 13:32:05,334] [INFO] Task started: Blastn
[2023-06-13 13:32:05,334] [INFO] Running command: blastn -query GCA_947475545.1_RH-23may17-645_genomic.fna/markers.fasta -db /var/lib/cwl/stg1389d4ca-b007-4ce0-86a6-336b393d7886/dqc_reference/reference_markers.fasta -out GCA_947475545.1_RH-23may17-645_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:32:06,082] [INFO] Task succeeded: Blastn
[2023-06-13 13:32:06,087] [INFO] Selected 28 target genomes.
[2023-06-13 13:32:06,087] [INFO] Target genome list was writen to GCA_947475545.1_RH-23may17-645_genomic.fna/target_genomes.txt
[2023-06-13 13:32:06,096] [INFO] Task started: fastANI
[2023-06-13 13:32:06,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg459d008a-4663-44ee-a2aa-13c98ce5482d/GCA_947475545.1_RH-23may17-645_genomic.fna.gz --refList GCA_947475545.1_RH-23may17-645_genomic.fna/target_genomes.txt --output GCA_947475545.1_RH-23may17-645_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:32:26,320] [INFO] Task succeeded: fastANI
[2023-06-13 13:32:26,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1389d4ca-b007-4ce0-86a6-336b393d7886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:32:26,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1389d4ca-b007-4ce0-86a6-336b393d7886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:32:26,344] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:32:26,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:32:26,345] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.4444	57	1058	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	75.3051	71	1058	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	75.1595	66	1058	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	75.0669	64	1058	95	below_threshold
Pseudonocardia abyssalis	strain=KRD168	GCA_019263705.2	2792008	2792008	type	True	75.0613	130	1058	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	75.0459	76	1058	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	75.0454	145	1058	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.0346	63	1058	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.9881	83	1058	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	74.969	134	1058	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	74.9492	54	1058	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.9185	154	1058	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	74.9172	72	1058	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	74.9069	148	1058	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	74.8922	186	1058	95	below_threshold
Kitasatospora viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	74.8816	209	1058	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	74.8778	65	1058	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.8105	148	1058	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	74.7936	78	1058	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	74.7673	79	1058	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:32:26,347] [INFO] DFAST Taxonomy check result was written to GCA_947475545.1_RH-23may17-645_genomic.fna/tc_result.tsv
[2023-06-13 13:32:26,348] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:32:26,348] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:32:26,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1389d4ca-b007-4ce0-86a6-336b393d7886/dqc_reference/checkm_data
[2023-06-13 13:32:26,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:32:26,387] [INFO] Task started: CheckM
[2023-06-13 13:32:26,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947475545.1_RH-23may17-645_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947475545.1_RH-23may17-645_genomic.fna/checkm_input GCA_947475545.1_RH-23may17-645_genomic.fna/checkm_result
[2023-06-13 13:33:01,400] [INFO] Task succeeded: CheckM
[2023-06-13 13:33:01,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:33:01,426] [INFO] ===== Completeness check finished =====
[2023-06-13 13:33:01,426] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:33:01,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947475545.1_RH-23may17-645_genomic.fna/markers.fasta)
[2023-06-13 13:33:01,427] [INFO] Task started: Blastn
[2023-06-13 13:33:01,427] [INFO] Running command: blastn -query GCA_947475545.1_RH-23may17-645_genomic.fna/markers.fasta -db /var/lib/cwl/stg1389d4ca-b007-4ce0-86a6-336b393d7886/dqc_reference/reference_markers_gtdb.fasta -out GCA_947475545.1_RH-23may17-645_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:33:02,419] [INFO] Task succeeded: Blastn
[2023-06-13 13:33:02,425] [INFO] Selected 24 target genomes.
[2023-06-13 13:33:02,425] [INFO] Target genome list was writen to GCA_947475545.1_RH-23may17-645_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:33:02,437] [INFO] Task started: fastANI
[2023-06-13 13:33:02,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg459d008a-4663-44ee-a2aa-13c98ce5482d/GCA_947475545.1_RH-23may17-645_genomic.fna.gz --refList GCA_947475545.1_RH-23may17-645_genomic.fna/target_genomes_gtdb.txt --output GCA_947475545.1_RH-23may17-645_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:33:14,473] [INFO] Task succeeded: fastANI
[2023-06-13 13:33:14,495] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:33:14,495] [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_903822495.1	s__CAIJPD01 sp903822495	93.8811	927	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIJPD01	95.0	99.94	99.94	0.97	0.97	2	-
GCA_903930745.1	s__CAIXZV01 sp903930745	77.9317	194	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIXZV01	95.0	99.19	99.11	0.83	0.82	3	-
GCA_016191345.1	s__UBA5189 sp016191345	77.917	271	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191395.1	s__UBA5189 sp016191395	77.8689	229	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297395.1	s__UBA5189 sp004297395	77.7863	260	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250155.1	s__UBA5189 sp003250155	77.7684	184	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	99.47	99.47	0.88	0.88	2	-
GCA_004298915.1	s__UBA5189 sp004298915	77.7669	161	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698095.1	s__CF-46 sp013698095	77.7098	243	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200665.1	s__UBA5189 sp016200665	77.6965	207	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026785.1	s__UBA5189 sp012026785	77.6927	244	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889475.1	s__UBA5189 sp005889475	77.6188	211	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200675.1	s__UBA5189 sp016200675	77.5792	222	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883615.1	s__CF-16 sp005883615	77.4154	164	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695255.1	s__JACDAV01 sp013695255	77.332	180	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__JACDAV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881915.1	s__Palsa-1033 sp017881915	77.3023	218	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695505.1	s__CF-46 sp013695505	77.2785	129	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881905.1	s__Chersky-267 sp017881905	77.1949	199	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Chersky-267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152165.1	s__Palsa-1033 sp003152165	77.1752	198	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881055.1	s__C-114 sp005881055	77.0328	147	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__C-114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860675.1	s__CTSoil-043 sp017860675	76.8235	136	1058	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CTSoil-043	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263705.1	s__Pseudonocardia sp019263705	75.045	129	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCA_019236545.1	s__Palsa-739 sp019236545	75.0158	57	1058	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	98.19	98.19	0.82	0.82	2	-
GCF_006385685.1	s__Amaricoccus solimangrovi	74.7673	79	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:33:14,497] [INFO] GTDB search result was written to GCA_947475545.1_RH-23may17-645_genomic.fna/result_gtdb.tsv
[2023-06-13 13:33:14,498] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:33:14,503] [INFO] DFAST_QC result json was written to GCA_947475545.1_RH-23may17-645_genomic.fna/dqc_result.json
[2023-06-13 13:33:14,503] [INFO] DFAST_QC completed!
[2023-06-13 13:33:14,503] [INFO] Total running time: 0h1m20s