[2024-01-24 13:02:03,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c85d73c-d39c-4240-b94a-4a10a69443b6/dqc_reference
[2024-01-24 13:02:04,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:04,873] [INFO] Task started: Prodigal
[2024-01-24 13:02:04,873] [INFO] Running command: gunzip -c /var/lib/cwl/stg16909824-3368-41d6-a5f5-f95f6c364e52/GCF_009697225.1_ASM969722v1_genomic.fna.gz | prodigal -d GCF_009697225.1_ASM969722v1_genomic.fna/cds.fna -a GCF_009697225.1_ASM969722v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:17,798] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:17,798] [INFO] Task started: HMMsearch
[2024-01-24 13:02:17,798] [INFO] Running command: hmmsearch --tblout GCF_009697225.1_ASM969722v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c85d73c-d39c-4240-b94a-4a10a69443b6/dqc_reference/reference_markers.hmm GCF_009697225.1_ASM969722v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:18,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:18,038] [INFO] Found 6/6 markers.
[2024-01-24 13:02:18,079] [INFO] Query marker FASTA was written to GCF_009697225.1_ASM969722v1_genomic.fna/markers.fasta
[2024-01-24 13:02:18,079] [INFO] Task started: Blastn
[2024-01-24 13:02:18,079] [INFO] Running command: blastn -query GCF_009697225.1_ASM969722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c85d73c-d39c-4240-b94a-4a10a69443b6/dqc_reference/reference_markers.fasta -out GCF_009697225.1_ASM969722v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:19,120] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:19,124] [INFO] Selected 22 target genomes.
[2024-01-24 13:02:19,124] [INFO] Target genome list was writen to GCF_009697225.1_ASM969722v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:19,132] [INFO] Task started: fastANI
[2024-01-24 13:02:19,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg16909824-3368-41d6-a5f5-f95f6c364e52/GCF_009697225.1_ASM969722v1_genomic.fna.gz --refList GCF_009697225.1_ASM969722v1_genomic.fna/target_genomes.txt --output GCF_009697225.1_ASM969722v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:37,125] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:37,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c85d73c-d39c-4240-b94a-4a10a69443b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:37,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c85d73c-d39c-4240-b94a-4a10a69443b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:37,143] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:37,143] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:37,143] [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
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	100.0	1508	1510	95	conclusive
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	80.9038	660	1510	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.4095	618	1510	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.9747	383	1510	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.9266	524	1510	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.8447	491	1510	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.8365	578	1510	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.8298	574	1510	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.7909	576	1510	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.7769	485	1510	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.7619	548	1510	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.6229	444	1510	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	78.4786	536	1510	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.431	478	1510	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	78.313	527	1510	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	78.2364	574	1510	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	78.1034	518	1510	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.0832	502	1510	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.0686	475	1510	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.007	421	1510	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.6986	354	1510	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	77.4768	446	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:37,145] [INFO] DFAST Taxonomy check result was written to GCF_009697225.1_ASM969722v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:37,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:37,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:37,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c85d73c-d39c-4240-b94a-4a10a69443b6/dqc_reference/checkm_data
[2024-01-24 13:02:37,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:37,192] [INFO] Task started: CheckM
[2024-01-24 13:02:37,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009697225.1_ASM969722v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009697225.1_ASM969722v1_genomic.fna/checkm_input GCF_009697225.1_ASM969722v1_genomic.fna/checkm_result
[2024-01-24 13:03:32,119] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:32,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:32,138] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:32,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:32,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009697225.1_ASM969722v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:32,138] [INFO] Task started: Blastn
[2024-01-24 13:03:32,138] [INFO] Running command: blastn -query GCF_009697225.1_ASM969722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c85d73c-d39c-4240-b94a-4a10a69443b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009697225.1_ASM969722v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:34,168] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:34,172] [INFO] Selected 19 target genomes.
[2024-01-24 13:03:34,172] [INFO] Target genome list was writen to GCF_009697225.1_ASM969722v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:34,207] [INFO] Task started: fastANI
[2024-01-24 13:03:34,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg16909824-3368-41d6-a5f5-f95f6c364e52/GCF_009697225.1_ASM969722v1_genomic.fna.gz --refList GCF_009697225.1_ASM969722v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009697225.1_ASM969722v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:51,369] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:51,384] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:51,384] [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_009697225.1	s__Halovulum marinum	100.0	1508	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013093415.1	s__Halovulum dunhuangense	80.8956	661	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265325.1	s__Halovulum sediminis	79.9407	642	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.1482	569	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.8473	570	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_008124525.1	s__Oceanicella actignis	78.7456	550	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.6601	440	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCA_015689685.1	s__HKCCE3408 sp015689685	78.6007	538	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	78.5379	554	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.3962	564	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834145.1	s__Roseovarius salinarum	78.3859	461	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	78.3062	548	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_006385685.1	s__Amaricoccus solimangrovi	78.2935	529	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	78.2113	578	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	78.2047	535	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.1459	650	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	78.1346	490	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	78.0513	606	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078595.1	s__Rhodobacter_B lobularis	77.8342	457	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:51,385] [INFO] GTDB search result was written to GCF_009697225.1_ASM969722v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:51,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:51,390] [INFO] DFAST_QC result json was written to GCF_009697225.1_ASM969722v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:51,390] [INFO] DFAST_QC completed!
[2024-01-24 13:03:51,390] [INFO] Total running time: 0h1m48s