[2024-01-24 13:36:32,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,147] [INFO] DQC Reference Directory: /var/lib/cwl/stge5292824-3454-430b-9750-4c3e6863f398/dqc_reference
[2024-01-24 13:36:33,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,469] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg93dca301-6893-49cb-94ec-e070971a18cf/GCF_014196635.1_ASM1419663v1_genomic.fna.gz | prodigal -d GCF_014196635.1_ASM1419663v1_genomic.fna/cds.fna -a GCF_014196635.1_ASM1419663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:44,027] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:44,028] [INFO] Task started: HMMsearch
[2024-01-24 13:36:44,028] [INFO] Running command: hmmsearch --tblout GCF_014196635.1_ASM1419663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5292824-3454-430b-9750-4c3e6863f398/dqc_reference/reference_markers.hmm GCF_014196635.1_ASM1419663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:44,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:44,312] [INFO] Found 6/6 markers.
[2024-01-24 13:36:44,349] [INFO] Query marker FASTA was written to GCF_014196635.1_ASM1419663v1_genomic.fna/markers.fasta
[2024-01-24 13:36:44,350] [INFO] Task started: Blastn
[2024-01-24 13:36:44,350] [INFO] Running command: blastn -query GCF_014196635.1_ASM1419663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5292824-3454-430b-9750-4c3e6863f398/dqc_reference/reference_markers.fasta -out GCF_014196635.1_ASM1419663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:45,159] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:45,162] [INFO] Selected 23 target genomes.
[2024-01-24 13:36:45,162] [INFO] Target genome list was writen to GCF_014196635.1_ASM1419663v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:45,170] [INFO] Task started: fastANI
[2024-01-24 13:36:45,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg93dca301-6893-49cb-94ec-e070971a18cf/GCF_014196635.1_ASM1419663v1_genomic.fna.gz --refList GCF_014196635.1_ASM1419663v1_genomic.fna/target_genomes.txt --output GCF_014196635.1_ASM1419663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:04,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:04,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5292824-3454-430b-9750-4c3e6863f398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:04,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5292824-3454-430b-9750-4c3e6863f398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:04,099] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:04,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:04,100] [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
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	100.0	1126	1129	95	conclusive
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	82.7266	590	1129	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	82.664	599	1129	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	82.3617	621	1129	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	82.3585	667	1129	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	82.3441	592	1129	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	82.2824	675	1129	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	82.2076	584	1129	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	82.1741	635	1129	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	82.1491	671	1129	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	82.1023	639	1129	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	82.0386	656	1129	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	82.0309	639	1129	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	82.0217	577	1129	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	82.016	594	1129	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	81.9571	594	1129	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	81.9451	648	1129	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	81.8633	614	1129	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	81.7505	608	1129	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.439	387	1129	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.3317	312	1129	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.9744	352	1129	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.9616	322	1129	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:04,101] [INFO] DFAST Taxonomy check result was written to GCF_014196635.1_ASM1419663v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:04,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:04,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:04,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5292824-3454-430b-9750-4c3e6863f398/dqc_reference/checkm_data
[2024-01-24 13:37:04,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:04,142] [INFO] Task started: CheckM
[2024-01-24 13:37:04,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196635.1_ASM1419663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196635.1_ASM1419663v1_genomic.fna/checkm_input GCF_014196635.1_ASM1419663v1_genomic.fna/checkm_result
[2024-01-24 13:37:40,499] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:40,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:40,523] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:40,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:40,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196635.1_ASM1419663v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:40,525] [INFO] Task started: Blastn
[2024-01-24 13:37:40,525] [INFO] Running command: blastn -query GCF_014196635.1_ASM1419663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5292824-3454-430b-9750-4c3e6863f398/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196635.1_ASM1419663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:42,076] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:42,079] [INFO] Selected 23 target genomes.
[2024-01-24 13:37:42,080] [INFO] Target genome list was writen to GCF_014196635.1_ASM1419663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:42,092] [INFO] Task started: fastANI
[2024-01-24 13:37:42,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg93dca301-6893-49cb-94ec-e070971a18cf/GCF_014196635.1_ASM1419663v1_genomic.fna.gz --refList GCF_014196635.1_ASM1419663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196635.1_ASM1419663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:02,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:02,490] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:02,490] [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_014196635.1	s__Sphingobium fontiphilum	100.0	1126	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009720145.1	s__Sphingobium sp009720145	82.8058	688	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508185.1	s__Sphingobium sp000508185	82.5694	601	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556865.1	s__Sphingobium sp001556865	82.3949	635	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000264945.2	s__Sphingobium indicum	82.3465	621	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_002355855.1	s__Sphingobium cloacae	82.3439	592	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002457415.1	s__Sphingobium sp002457415	82.301	586	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710155.1	s__Sphingobium limneticum	82.2728	677	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	82.1777	614	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_007830065.1	s__Sphingobium wenxiniae	82.0204	594	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	-
GCF_001563265.1	s__Sphingobium sp001563265	82.005	672	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.38	97.84	0.74	0.68	3	-
GCF_008692605.1	s__Sphingobium estronivorans	81.9916	591	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375535.1	s__Sphingobium sp013375535	81.9515	679	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152845.1	s__Sphingobium fuliginis	81.9285	650	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_900111125.1	s__Sphingobium sp900111125	81.8661	675	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967075.1	s__Sphingobium amiense	81.8642	617	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013375555.1	s__Sphingobium sp013375555	81.7253	603	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	81.6722	638	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911745.1	s__Sphingobium sp013911745	81.5359	482	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361945.1	s__Sphingobium barthaii_A	81.4423	572	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456115.1	s__Sphingobium baderi_A	81.2254	600	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080435.1	s__Sphingobium herbicidovorans	81.1269	539	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_900218065.1	s__Sphingobium sp900218065	80.9614	519	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.42	97.40	0.85	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:02,492] [INFO] GTDB search result was written to GCF_014196635.1_ASM1419663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:02,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:02,500] [INFO] DFAST_QC result json was written to GCF_014196635.1_ASM1419663v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:02,500] [INFO] DFAST_QC completed!
[2024-01-24 13:38:02,500] [INFO] Total running time: 0h1m30s