[2024-01-24 13:22:55,512] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,514] [INFO] DQC Reference Directory: /var/lib/cwl/stgdef24c77-7f53-46b8-bf23-fc5fcf1b72b0/dqc_reference
[2024-01-24 13:22:56,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,820] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f955f8e-174f-45d5-9b51-2d9c932b3498/GCF_003550175.1_ASM355017v1_genomic.fna.gz | prodigal -d GCF_003550175.1_ASM355017v1_genomic.fna/cds.fna -a GCF_003550175.1_ASM355017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:06,272] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:06,273] [INFO] Task started: HMMsearch
[2024-01-24 13:23:06,273] [INFO] Running command: hmmsearch --tblout GCF_003550175.1_ASM355017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdef24c77-7f53-46b8-bf23-fc5fcf1b72b0/dqc_reference/reference_markers.hmm GCF_003550175.1_ASM355017v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:06,554] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:06,556] [INFO] Found 6/6 markers.
[2024-01-24 13:23:06,583] [INFO] Query marker FASTA was written to GCF_003550175.1_ASM355017v1_genomic.fna/markers.fasta
[2024-01-24 13:23:06,584] [INFO] Task started: Blastn
[2024-01-24 13:23:06,584] [INFO] Running command: blastn -query GCF_003550175.1_ASM355017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef24c77-7f53-46b8-bf23-fc5fcf1b72b0/dqc_reference/reference_markers.fasta -out GCF_003550175.1_ASM355017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:07,570] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:07,574] [INFO] Selected 29 target genomes.
[2024-01-24 13:23:07,574] [INFO] Target genome list was writen to GCF_003550175.1_ASM355017v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:07,610] [INFO] Task started: fastANI
[2024-01-24 13:23:07,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f955f8e-174f-45d5-9b51-2d9c932b3498/GCF_003550175.1_ASM355017v1_genomic.fna.gz --refList GCF_003550175.1_ASM355017v1_genomic.fna/target_genomes.txt --output GCF_003550175.1_ASM355017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:27,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:27,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdef24c77-7f53-46b8-bf23-fc5fcf1b72b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:27,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdef24c77-7f53-46b8-bf23-fc5fcf1b72b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:27,159] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:27,160] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:27,160] [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
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	100.0	990	992	95	conclusive
Methyloceanibacter stevinii	strain=R-67176	GCA_001723355.1	1774970	1774970	type	True	77.179	103	992	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.1445	138	992	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.1168	177	992	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.1034	178	992	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	76.9906	109	992	95	below_threshold
Methyloceanibacter caenitepidi	strain=Gela4	GCA_000828475.1	1384459	1384459	type	True	76.9737	113	992	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.9023	155	992	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	76.8372	163	992	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.8242	148	992	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	76.8054	221	992	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.7927	184	992	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	76.7503	110	992	95	below_threshold
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	76.7143	155	992	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	76.7042	154	992	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	76.6738	143	992	95	below_threshold
Rhodomicrobium udaipurense	strain=JA643	GCA_016461795.1	1202716	1202716	type	True	76.6555	130	992	95	below_threshold
Rhodomicrobium lacus	strain=JA980	GCA_003992725.1	2498452	2498452	type	True	76.6015	132	992	95	below_threshold
Rhodomicrobium udaipurense	strain=JA643	GCA_000636015.1	1202716	1202716	type	True	76.5733	127	992	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.566	112	992	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.5438	122	992	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.5089	181	992	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.3766	129	992	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	76.3766	128	992	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	76.2573	153	992	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.2247	134	992	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1938	90	992	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	76.1086	148	992	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.8919	115	992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:27,162] [INFO] DFAST Taxonomy check result was written to GCF_003550175.1_ASM355017v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:27,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:27,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:27,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdef24c77-7f53-46b8-bf23-fc5fcf1b72b0/dqc_reference/checkm_data
[2024-01-24 13:23:27,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:27,208] [INFO] Task started: CheckM
[2024-01-24 13:23:27,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003550175.1_ASM355017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003550175.1_ASM355017v1_genomic.fna/checkm_input GCF_003550175.1_ASM355017v1_genomic.fna/checkm_result
[2024-01-24 13:23:57,309] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:57,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:57,331] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:57,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:57,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003550175.1_ASM355017v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:57,332] [INFO] Task started: Blastn
[2024-01-24 13:23:57,332] [INFO] Running command: blastn -query GCF_003550175.1_ASM355017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef24c77-7f53-46b8-bf23-fc5fcf1b72b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003550175.1_ASM355017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:59,200] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:59,205] [INFO] Selected 27 target genomes.
[2024-01-24 13:23:59,206] [INFO] Target genome list was writen to GCF_003550175.1_ASM355017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:59,256] [INFO] Task started: fastANI
[2024-01-24 13:23:59,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f955f8e-174f-45d5-9b51-2d9c932b3498/GCF_003550175.1_ASM355017v1_genomic.fna.gz --refList GCF_003550175.1_ASM355017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003550175.1_ASM355017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:16,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:16,089] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:16,089] [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_003550175.1	s__Dichotomicrobium thermohalophilum	100.0	990	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Dichotomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001723355.1	s__Methyloceanibacter stevinii	77.179	103	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708035.1	s__Hyphomicrobium_A sp009708035	77.1454	137	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198715.1	s__R-RK-3 sp002198715	77.1337	239	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__R-RK-3	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003966715.1	s__Blastochloris tepida	77.087	180	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	77.0858	149	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117445.1	s__Hyphomicrobium_A sp900117445	77.046	90	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828475.1	s__Methyloceanibacter caenitepidi	76.9737	113	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013341275.1	s__Methyloligella sp013341275	76.8781	136	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloligella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117455.1	s__Hyphomicrobium sp900117455	76.855	114	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	76.8425	129	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	76.8372	163	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796995.1	s__Allorhizobium sp002796995	76.8199	113	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCA_008933705.1	s__AWTP1-13 sp008933705	76.8106	156	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	76.7953	184	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015482775.1	s__Kaustia mangrovi	76.7953	222	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992725.1	s__Rhodomicrobium lacus	76.6015	132	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	76.5581	121	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148505.1	s__Pseudoxanthobacter soli	76.5577	164	992	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	76.4132	167	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	76.3407	110	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCF_017815135.1	s__Jiella sp017815135	76.2985	133	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	76.231	102	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	76.1556	92	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825785.1	s__Hyphomicrobium sp902825785	76.0057	67	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644005.1	s__RCIO01 sp017644005	75.9621	96	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164825.1	s__Roseiarcus sp003164825	75.8378	90	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	98.98	98.92	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:16,092] [INFO] GTDB search result was written to GCF_003550175.1_ASM355017v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:16,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:16,097] [INFO] DFAST_QC result json was written to GCF_003550175.1_ASM355017v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:16,097] [INFO] DFAST_QC completed!
[2024-01-24 13:24:16,097] [INFO] Total running time: 0h1m21s