[2024-01-24 12:14:33,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,665] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfe39b64-75ab-44af-b9b0-4b5e1d47e1d5/dqc_reference
[2024-01-24 12:14:34,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,989] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,990] [INFO] Running command: gunzip -c /var/lib/cwl/stg052cdd88-87ae-44ce-83e6-90bda60227ef/GCF_003590945.1_ASM359094v1_genomic.fna.gz | prodigal -d GCF_003590945.1_ASM359094v1_genomic.fna/cds.fna -a GCF_003590945.1_ASM359094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:49,758] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:49,758] [INFO] Task started: HMMsearch
[2024-01-24 12:14:49,758] [INFO] Running command: hmmsearch --tblout GCF_003590945.1_ASM359094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfe39b64-75ab-44af-b9b0-4b5e1d47e1d5/dqc_reference/reference_markers.hmm GCF_003590945.1_ASM359094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:49,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:49,996] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg052cdd88-87ae-44ce-83e6-90bda60227ef/GCF_003590945.1_ASM359094v1_genomic.fna.gz]
[2024-01-24 12:14:50,039] [INFO] Query marker FASTA was written to GCF_003590945.1_ASM359094v1_genomic.fna/markers.fasta
[2024-01-24 12:14:50,039] [INFO] Task started: Blastn
[2024-01-24 12:14:50,039] [INFO] Running command: blastn -query GCF_003590945.1_ASM359094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe39b64-75ab-44af-b9b0-4b5e1d47e1d5/dqc_reference/reference_markers.fasta -out GCF_003590945.1_ASM359094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:50,875] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:50,878] [INFO] Selected 26 target genomes.
[2024-01-24 12:14:50,878] [INFO] Target genome list was writen to GCF_003590945.1_ASM359094v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:50,885] [INFO] Task started: fastANI
[2024-01-24 12:14:50,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg052cdd88-87ae-44ce-83e6-90bda60227ef/GCF_003590945.1_ASM359094v1_genomic.fna.gz --refList GCF_003590945.1_ASM359094v1_genomic.fna/target_genomes.txt --output GCF_003590945.1_ASM359094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:16,180] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:16,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfe39b64-75ab-44af-b9b0-4b5e1d47e1d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:16,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfe39b64-75ab-44af-b9b0-4b5e1d47e1d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:16,195] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:16,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:16,195] [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
Zavarzinia compransoris	strain=DSM 1231	GCA_004362995.1	1264899	1264899	type	True	81.5861	937	1866	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	81.508	956	1866	95	below_threshold
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	81.2411	920	1866	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	77.199	315	1866	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	77.1927	418	1866	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	77.1635	453	1866	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.1372	280	1866	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.9892	404	1866	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.9786	296	1866	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.9208	288	1866	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.9056	296	1866	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.8999	166	1866	95	below_threshold
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	76.832	258	1866	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.7878	448	1866	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	76.766	254	1866	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	76.6605	304	1866	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	76.6045	369	1866	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.602	348	1866	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.5435	380	1866	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	76.5331	158	1866	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.5291	227	1866	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.5194	254	1866	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.3944	398	1866	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.2854	251	1866	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.27	157	1866	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	76.2429	143	1866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:16,197] [INFO] DFAST Taxonomy check result was written to GCF_003590945.1_ASM359094v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:16,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:16,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:16,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfe39b64-75ab-44af-b9b0-4b5e1d47e1d5/dqc_reference/checkm_data
[2024-01-24 12:15:16,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:16,251] [INFO] Task started: CheckM
[2024-01-24 12:15:16,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590945.1_ASM359094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590945.1_ASM359094v1_genomic.fna/checkm_input GCF_003590945.1_ASM359094v1_genomic.fna/checkm_result
[2024-01-24 12:16:01,347] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:01,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:01,362] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:01,362] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:01,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590945.1_ASM359094v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:01,363] [INFO] Task started: Blastn
[2024-01-24 12:16:01,363] [INFO] Running command: blastn -query GCF_003590945.1_ASM359094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe39b64-75ab-44af-b9b0-4b5e1d47e1d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590945.1_ASM359094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:02,998] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:03,001] [INFO] Selected 23 target genomes.
[2024-01-24 12:16:03,001] [INFO] Target genome list was writen to GCF_003590945.1_ASM359094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:03,012] [INFO] Task started: fastANI
[2024-01-24 12:16:03,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg052cdd88-87ae-44ce-83e6-90bda60227ef/GCF_003590945.1_ASM359094v1_genomic.fna.gz --refList GCF_003590945.1_ASM359094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003590945.1_ASM359094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:28,038] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:28,052] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:28,052] [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_003590945.1	s__Zavarzinia sp003590945	100.0	1863	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003173055.1	s__Zavarzinia compransoris	81.4736	962	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003173035.1	s__Zavarzinia aquatilis	81.2237	921	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923315.1	s__Azospirillum sp003116065	77.1224	440	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.9768	508	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	76.9526	474	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901915.1	s__Phaeospirillum sp903901915	76.8862	263	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.99	99.99	0.95	0.95	2	-
GCF_900177295.1	s__Tistlia consotensis	76.8697	506	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001402875.1	s__Blastochloris viridis	76.8186	255	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	100.00	100.00	1.00	1.00	3	-
GCA_016716745.1	s__GCA-013693735 sp016716745	76.8066	254	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	76.7735	450	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124315.1	s__RI-34 sp016124315	76.7654	257	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXS01;f__SMXS01;g__RI-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	76.7593	421	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.658	268	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_016869375.1	s__SHVZ01 sp016869375	76.6077	253	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	76.4156	393	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899885.1	s__CAIULK01 sp903899885	76.3581	145	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAIULK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	76.3555	312	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_003951315.1	s__Sphingomonas sp003951315	76.3101	215	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.3086	219	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	76.223	160	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_019241915.1	s__AP-15 sp019241915	76.0112	141	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	75.7409	217	1866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:28,055] [INFO] GTDB search result was written to GCF_003590945.1_ASM359094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:28,056] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:28,060] [INFO] DFAST_QC result json was written to GCF_003590945.1_ASM359094v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:28,060] [INFO] DFAST_QC completed!
[2024-01-24 12:16:28,060] [INFO] Total running time: 0h1m54s