[2024-01-25 19:00:50,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:50,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:50,607] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd6d606c-2946-479f-8ba1-8a5a0938a327/dqc_reference
[2024-01-25 19:00:51,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:51,786] [INFO] Task started: Prodigal
[2024-01-25 19:00:51,786] [INFO] Running command: gunzip -c /var/lib/cwl/stgec390502-b895-4476-9184-e71b7d9eceda/GCF_023487995.1_ASM2348799v1_genomic.fna.gz | prodigal -d GCF_023487995.1_ASM2348799v1_genomic.fna/cds.fna -a GCF_023487995.1_ASM2348799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:02,577] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:02,577] [INFO] Task started: HMMsearch
[2024-01-25 19:01:02,577] [INFO] Running command: hmmsearch --tblout GCF_023487995.1_ASM2348799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd6d606c-2946-479f-8ba1-8a5a0938a327/dqc_reference/reference_markers.hmm GCF_023487995.1_ASM2348799v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:02,801] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:02,802] [INFO] Found 6/6 markers.
[2024-01-25 19:01:02,836] [INFO] Query marker FASTA was written to GCF_023487995.1_ASM2348799v1_genomic.fna/markers.fasta
[2024-01-25 19:01:02,836] [INFO] Task started: Blastn
[2024-01-25 19:01:02,836] [INFO] Running command: blastn -query GCF_023487995.1_ASM2348799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6d606c-2946-479f-8ba1-8a5a0938a327/dqc_reference/reference_markers.fasta -out GCF_023487995.1_ASM2348799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:03,800] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:03,802] [INFO] Selected 23 target genomes.
[2024-01-25 19:01:03,803] [INFO] Target genome list was writen to GCF_023487995.1_ASM2348799v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:03,819] [INFO] Task started: fastANI
[2024-01-25 19:01:03,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgec390502-b895-4476-9184-e71b7d9eceda/GCF_023487995.1_ASM2348799v1_genomic.fna.gz --refList GCF_023487995.1_ASM2348799v1_genomic.fna/target_genomes.txt --output GCF_023487995.1_ASM2348799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:24,215] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:24,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd6d606c-2946-479f-8ba1-8a5a0938a327/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:24,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd6d606c-2946-479f-8ba1-8a5a0938a327/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:24,229] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:01:24,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:01:24,229] [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
Thermohalobaculum xanthum	strain=M0105	GCA_016623495.1	2753746	2753746	type	True	83.9419	991	1417	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.6515	535	1417	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.3889	435	1417	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.3117	482	1417	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.1397	356	1417	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.1313	365	1417	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	78.0989	476	1417	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	78.0775	536	1417	95	below_threshold
Coraliihabitans acroporae	strain=NNCM2	GCA_019891535.1	2834412	2834412	type	True	78.077	438	1417	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.0659	364	1417	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	78.0608	590	1417	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.8996	422	1417	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.8357	379	1417	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.8291	371	1417	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	77.7804	372	1417	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.7765	443	1417	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.7489	371	1417	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	77.7076	368	1417	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.598	337	1417	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	77.5258	358	1417	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	77.4916	362	1417	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.2819	320	1417	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.2758	425	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:24,231] [INFO] DFAST Taxonomy check result was written to GCF_023487995.1_ASM2348799v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:24,232] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:24,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:24,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd6d606c-2946-479f-8ba1-8a5a0938a327/dqc_reference/checkm_data
[2024-01-25 19:01:24,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:24,296] [INFO] Task started: CheckM
[2024-01-25 19:01:24,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023487995.1_ASM2348799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023487995.1_ASM2348799v1_genomic.fna/checkm_input GCF_023487995.1_ASM2348799v1_genomic.fna/checkm_result
[2024-01-25 19:02:06,790] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:06,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:06,810] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:06,810] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:06,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023487995.1_ASM2348799v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:06,811] [INFO] Task started: Blastn
[2024-01-25 19:02:06,811] [INFO] Running command: blastn -query GCF_023487995.1_ASM2348799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6d606c-2946-479f-8ba1-8a5a0938a327/dqc_reference/reference_markers_gtdb.fasta -out GCF_023487995.1_ASM2348799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:08,765] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:08,768] [INFO] Selected 21 target genomes.
[2024-01-25 19:02:08,768] [INFO] Target genome list was writen to GCF_023487995.1_ASM2348799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:08,797] [INFO] Task started: fastANI
[2024-01-25 19:02:08,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgec390502-b895-4476-9184-e71b7d9eceda/GCF_023487995.1_ASM2348799v1_genomic.fna.gz --refList GCF_023487995.1_ASM2348799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023487995.1_ASM2348799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:26,584] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:26,596] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:02:26,596] [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_016623495.1	s__Limibaculum sp016623495	83.9652	989	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	78.698	529	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_013093415.1	s__Halovulum dunhuangense	78.3871	435	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	78.3015	483	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	78.1953	532	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	78.1058	358	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	78.0853	390	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCF_900113695.1	s__Albimonas pacifica	78.0207	596	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119835.1	s__SKOX01 sp007119835	77.909	289	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SKOX01	95.0	99.00	98.89	0.80	0.77	3	-
GCF_004342445.1	s__Rhodovulum euryhalinum	77.9088	421	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	77.7951	456	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995835.1	s__Amaricoccus sp017995835	77.7941	352	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697125.1	s__J013 sp003697125	77.7862	407	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__J013	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	77.7263	450	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	77.7256	366	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	77.7175	368	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	77.705	467	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	77.5695	259	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550665.1	s__Rhodobaculum sp003550665	77.4692	299	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.32	99.19	0.86	0.85	4	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.4284	508	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131685.1	s__Rhodobaculum sp007131685	77.2787	278	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.44	99.41	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:26,598] [INFO] GTDB search result was written to GCF_023487995.1_ASM2348799v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:26,598] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:26,602] [INFO] DFAST_QC result json was written to GCF_023487995.1_ASM2348799v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:26,603] [INFO] DFAST_QC completed!
[2024-01-25 19:02:26,603] [INFO] Total running time: 0h1m36s