[2024-01-24 12:40:08,351] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg81b59808-f0fd-4e6a-8783-ff26675732fa/dqc_reference
[2024-01-24 12:40:09,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,722] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgef0b4f9d-c520-42a4-bf08-40fb8803f491/GCF_003234965.1_ASM323496v1_genomic.fna.gz | prodigal -d GCF_003234965.1_ASM323496v1_genomic.fna/cds.fna -a GCF_003234965.1_ASM323496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:24,022] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:24,022] [INFO] Task started: HMMsearch
[2024-01-24 12:40:24,023] [INFO] Running command: hmmsearch --tblout GCF_003234965.1_ASM323496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81b59808-f0fd-4e6a-8783-ff26675732fa/dqc_reference/reference_markers.hmm GCF_003234965.1_ASM323496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:24,306] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:24,308] [INFO] Found 6/6 markers.
[2024-01-24 12:40:24,350] [INFO] Query marker FASTA was written to GCF_003234965.1_ASM323496v1_genomic.fna/markers.fasta
[2024-01-24 12:40:24,351] [INFO] Task started: Blastn
[2024-01-24 12:40:24,351] [INFO] Running command: blastn -query GCF_003234965.1_ASM323496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b59808-f0fd-4e6a-8783-ff26675732fa/dqc_reference/reference_markers.fasta -out GCF_003234965.1_ASM323496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:25,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:25,491] [INFO] Selected 29 target genomes.
[2024-01-24 12:40:25,491] [INFO] Target genome list was writen to GCF_003234965.1_ASM323496v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:25,505] [INFO] Task started: fastANI
[2024-01-24 12:40:25,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0b4f9d-c520-42a4-bf08-40fb8803f491/GCF_003234965.1_ASM323496v1_genomic.fna.gz --refList GCF_003234965.1_ASM323496v1_genomic.fna/target_genomes.txt --output GCF_003234965.1_ASM323496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:52,832] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:52,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81b59808-f0fd-4e6a-8783-ff26675732fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:52,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81b59808-f0fd-4e6a-8783-ff26675732fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:52,860] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:52,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:52,860] [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
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	100.0	1398	1399	95	conclusive
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.5904	361	1399	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.5402	277	1399	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	77.4953	284	1399	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.4691	283	1399	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.4204	294	1399	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	77.4156	285	1399	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	77.3064	351	1399	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	77.2899	323	1399	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.2745	280	1399	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.2273	294	1399	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	77.2094	301	1399	95	below_threshold
Methylobacterium haplocladii	strain=NBRC 107714	GCA_007992175.1	1176176	1176176	type	True	77.1926	210	1399	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	77.1785	303	1399	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.1766	263	1399	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	77.1714	282	1399	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	77.1005	198	1399	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.0998	265	1399	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.0781	275	1399	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	77.0158	282	1399	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	76.9998	239	1399	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.912	290	1399	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	76.8965	261	1399	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	76.795	254	1399	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.6647	156	1399	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	76.536	239	1399	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	76.5105	232	1399	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.4704	294	1399	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.319	248	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:52,864] [INFO] DFAST Taxonomy check result was written to GCF_003234965.1_ASM323496v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:52,864] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:52,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:52,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81b59808-f0fd-4e6a-8783-ff26675732fa/dqc_reference/checkm_data
[2024-01-24 12:40:52,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:52,910] [INFO] Task started: CheckM
[2024-01-24 12:40:52,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003234965.1_ASM323496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003234965.1_ASM323496v1_genomic.fna/checkm_input GCF_003234965.1_ASM323496v1_genomic.fna/checkm_result
[2024-01-24 12:42:03,654] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:03,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:03,680] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:03,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:03,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003234965.1_ASM323496v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:03,681] [INFO] Task started: Blastn
[2024-01-24 12:42:03,681] [INFO] Running command: blastn -query GCF_003234965.1_ASM323496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b59808-f0fd-4e6a-8783-ff26675732fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003234965.1_ASM323496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:05,770] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:05,777] [INFO] Selected 15 target genomes.
[2024-01-24 12:42:05,777] [INFO] Target genome list was writen to GCF_003234965.1_ASM323496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:05,788] [INFO] Task started: fastANI
[2024-01-24 12:42:05,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0b4f9d-c520-42a4-bf08-40fb8803f491/GCF_003234965.1_ASM323496v1_genomic.fna.gz --refList GCF_003234965.1_ASM323496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003234965.1_ASM323496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:18,716] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:18,733] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:18,733] [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_003234965.1	s__Aestuariivirga litoralis	100.0	1398	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903930095.1	s__Aestuariivirga sp903930095	82.8046	573	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900298995.1	s__Aestuariivirga sp900298995	80.9348	644	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185245.1	s__Aestuariivirga sp016185245	79.5083	559	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	99.81	99.81	0.97	0.97	2	-
GCA_016710435.1	s__Aestuariivirga sp016710435	78.8587	449	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576695.1	s__Nordella sp003576695	78.8536	547	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595235.1	s__Nordella sp016595235	78.4915	546	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873435.1	s__Nordella sp014873435	78.4197	481	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032065.1	s__Aestuariivirga sp012032065	78.302	293	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793355.1	s__JAEUMG01 sp016793355	77.9248	345	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__JAEUMG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380505.1	s__Aestuariivirga sp014380505	77.6465	222	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	77.3429	281	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	77.3395	313	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653715.1	s__Methylobacterium platani	77.1705	302	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_008000895.1	s__Methylobacterium sp008000895	76.7533	215	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	98.22	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:18,735] [INFO] GTDB search result was written to GCF_003234965.1_ASM323496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:18,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:18,741] [INFO] DFAST_QC result json was written to GCF_003234965.1_ASM323496v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:18,741] [INFO] DFAST_QC completed!
[2024-01-24 12:42:18,741] [INFO] Total running time: 0h2m10s