[2024-01-24 12:46:57,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,158] [INFO] DQC Reference Directory: /var/lib/cwl/stga8ddaebb-4fe6-493d-9414-476bbbd81a3a/dqc_reference
[2024-01-24 12:46:58,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:58,574] [INFO] Task started: Prodigal
[2024-01-24 12:46:58,574] [INFO] Running command: gunzip -c /var/lib/cwl/stge4b1aaa4-89d0-4e3b-a4e0-db3af09ac9f4/GCF_003012815.1_ASM301281v1_genomic.fna.gz | prodigal -d GCF_003012815.1_ASM301281v1_genomic.fna/cds.fna -a GCF_003012815.1_ASM301281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:05,937] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:05,938] [INFO] Task started: HMMsearch
[2024-01-24 12:47:05,938] [INFO] Running command: hmmsearch --tblout GCF_003012815.1_ASM301281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8ddaebb-4fe6-493d-9414-476bbbd81a3a/dqc_reference/reference_markers.hmm GCF_003012815.1_ASM301281v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:06,193] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:06,195] [INFO] Found 6/6 markers.
[2024-01-24 12:47:06,217] [INFO] Query marker FASTA was written to GCF_003012815.1_ASM301281v1_genomic.fna/markers.fasta
[2024-01-24 12:47:06,218] [INFO] Task started: Blastn
[2024-01-24 12:47:06,218] [INFO] Running command: blastn -query GCF_003012815.1_ASM301281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8ddaebb-4fe6-493d-9414-476bbbd81a3a/dqc_reference/reference_markers.fasta -out GCF_003012815.1_ASM301281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:07,075] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:07,084] [INFO] Selected 29 target genomes.
[2024-01-24 12:47:07,085] [INFO] Target genome list was writen to GCF_003012815.1_ASM301281v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:07,093] [INFO] Task started: fastANI
[2024-01-24 12:47:07,094] [INFO] Running command: fastANI --query /var/lib/cwl/stge4b1aaa4-89d0-4e3b-a4e0-db3af09ac9f4/GCF_003012815.1_ASM301281v1_genomic.fna.gz --refList GCF_003012815.1_ASM301281v1_genomic.fna/target_genomes.txt --output GCF_003012815.1_ASM301281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:26,802] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:26,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8ddaebb-4fe6-493d-9414-476bbbd81a3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:26,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8ddaebb-4fe6-493d-9414-476bbbd81a3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:26,838] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:26,839] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:26,839] [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
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	79.0839	378	833	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.6434	348	833	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	78.6126	240	833	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	78.514	347	833	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.4451	324	833	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.3166	265	833	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.3009	276	833	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.2196	322	833	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.1434	219	833	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.0819	224	833	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.0789	206	833	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	78.0688	236	833	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	78.0356	262	833	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.0093	282	833	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	78.0048	282	833	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	78.0008	237	833	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	77.9926	262	833	95	below_threshold
Sphingobium bisphenolivorans	strain=YL23	GCA_000412635.1	1335760	1335760	type	True	77.9743	221	833	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	77.9599	221	833	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	77.9454	260	833	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.8899	215	833	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	77.8532	177	833	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.8517	286	833	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.6957	243	833	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	77.6097	203	833	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.5149	217	833	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.4792	216	833	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	77.4362	156	833	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	77.4225	157	833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:26,842] [INFO] DFAST Taxonomy check result was written to GCF_003012815.1_ASM301281v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:26,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:26,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:26,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8ddaebb-4fe6-493d-9414-476bbbd81a3a/dqc_reference/checkm_data
[2024-01-24 12:47:26,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:26,876] [INFO] Task started: CheckM
[2024-01-24 12:47:26,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012815.1_ASM301281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012815.1_ASM301281v1_genomic.fna/checkm_input GCF_003012815.1_ASM301281v1_genomic.fna/checkm_result
[2024-01-24 12:47:54,498] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:54,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:54,520] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:54,520] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:54,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012815.1_ASM301281v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:54,521] [INFO] Task started: Blastn
[2024-01-24 12:47:54,521] [INFO] Running command: blastn -query GCF_003012815.1_ASM301281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8ddaebb-4fe6-493d-9414-476bbbd81a3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012815.1_ASM301281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:56,091] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:56,095] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:56,096] [INFO] Target genome list was writen to GCF_003012815.1_ASM301281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:56,133] [INFO] Task started: fastANI
[2024-01-24 12:47:56,133] [INFO] Running command: fastANI --query /var/lib/cwl/stge4b1aaa4-89d0-4e3b-a4e0-db3af09ac9f4/GCF_003012815.1_ASM301281v1_genomic.fna.gz --refList GCF_003012815.1_ASM301281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012815.1_ASM301281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:10,189] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:10,212] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:10,212] [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_003012815.1	s__Allosphingosinicella vermicomposti	100.0	833	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016025255.1	s__Allosphingosinicella sp016025255	83.2208	558	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	79.1886	357	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	79.1206	375	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806315.1	s__Allosphingosinicella sp902806315	78.794	323	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	78.626	349	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	78.6131	240	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012735.1	s__Allosphingosinicella deserti	78.5151	347	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	78.4628	322	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCA_005882415.1	s__Allosphingosinicella sp005882415	78.4066	297	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	78.2668	306	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383095.1	s__Sphingomonas_N sp000383095	78.2563	272	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315525.1	s__Sphingobium yanoikuyae	78.0187	280	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_003967075.1	s__Sphingobium amiense	77.9945	262	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004151485.1	s__Allosphingosinicella sp004151485	77.9939	295	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	77.8898	215	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	77.8409	287	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781555.1	s__Allosphingosinicella sp016781555	77.7386	172	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984035.1	s__Sphingopyxis sp001984035	77.6744	258	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	77.4554	183	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:10,216] [INFO] GTDB search result was written to GCF_003012815.1_ASM301281v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:10,217] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:10,225] [INFO] DFAST_QC result json was written to GCF_003012815.1_ASM301281v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:10,225] [INFO] DFAST_QC completed!
[2024-01-24 12:48:10,225] [INFO] Total running time: 0h1m13s