[2024-01-24 12:42:06,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:06,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:06,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3b6c449-54e2-4cb2-97d8-1dbe74efa96d/dqc_reference
[2024-01-24 12:42:07,552] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:07,553] [INFO] Task started: Prodigal
[2024-01-24 12:42:07,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg01760437-aa54-44eb-83b9-06094cb35319/GCF_000622425.1_32187_draft_genomic.fna.gz | prodigal -d GCF_000622425.1_32187_draft_genomic.fna/cds.fna -a GCF_000622425.1_32187_draft_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:20,153] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:20,153] [INFO] Task started: HMMsearch
[2024-01-24 12:42:20,153] [INFO] Running command: hmmsearch --tblout GCF_000622425.1_32187_draft_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3b6c449-54e2-4cb2-97d8-1dbe74efa96d/dqc_reference/reference_markers.hmm GCF_000622425.1_32187_draft_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:20,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:20,459] [INFO] Found 6/6 markers.
[2024-01-24 12:42:20,495] [INFO] Query marker FASTA was written to GCF_000622425.1_32187_draft_genomic.fna/markers.fasta
[2024-01-24 12:42:20,495] [INFO] Task started: Blastn
[2024-01-24 12:42:20,495] [INFO] Running command: blastn -query GCF_000622425.1_32187_draft_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3b6c449-54e2-4cb2-97d8-1dbe74efa96d/dqc_reference/reference_markers.fasta -out GCF_000622425.1_32187_draft_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:21,181] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:21,185] [INFO] Selected 23 target genomes.
[2024-01-24 12:42:21,186] [INFO] Target genome list was writen to GCF_000622425.1_32187_draft_genomic.fna/target_genomes.txt
[2024-01-24 12:42:21,195] [INFO] Task started: fastANI
[2024-01-24 12:42:21,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg01760437-aa54-44eb-83b9-06094cb35319/GCF_000622425.1_32187_draft_genomic.fna.gz --refList GCF_000622425.1_32187_draft_genomic.fna/target_genomes.txt --output GCF_000622425.1_32187_draft_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:35,876] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:35,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3b6c449-54e2-4cb2-97d8-1dbe74efa96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:35,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3b6c449-54e2-4cb2-97d8-1dbe74efa96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:35,898] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:35,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:35,899] [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
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	99.9951	1320	1323	95	conclusive
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	78.0283	357	1323	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	78.0245	379	1323	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.9252	348	1323	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.476	255	1323	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.4485	295	1323	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.411	254	1323	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.3444	265	1323	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.3319	241	1323	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.3106	220	1323	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.2277	229	1323	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.1972	222	1323	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	76.9208	260	1323	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	76.7618	225	1323	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.7487	89	1323	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.4829	151	1323	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.4205	97	1323	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	76.3794	62	1323	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	76.2744	107	1323	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.2527	93	1323	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.2429	104	1323	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	76.0821	108	1323	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	75.9549	125	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:35,900] [INFO] DFAST Taxonomy check result was written to GCF_000622425.1_32187_draft_genomic.fna/tc_result.tsv
[2024-01-24 12:42:35,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:35,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:35,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3b6c449-54e2-4cb2-97d8-1dbe74efa96d/dqc_reference/checkm_data
[2024-01-24 12:42:35,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:35,941] [INFO] Task started: CheckM
[2024-01-24 12:42:35,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000622425.1_32187_draft_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000622425.1_32187_draft_genomic.fna/checkm_input GCF_000622425.1_32187_draft_genomic.fna/checkm_result
[2024-01-24 12:43:15,309] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:15,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:15,332] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:15,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:15,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000622425.1_32187_draft_genomic.fna/markers.fasta)
[2024-01-24 12:43:15,333] [INFO] Task started: Blastn
[2024-01-24 12:43:15,333] [INFO] Running command: blastn -query GCF_000622425.1_32187_draft_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3b6c449-54e2-4cb2-97d8-1dbe74efa96d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000622425.1_32187_draft_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:16,349] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:16,353] [INFO] Selected 21 target genomes.
[2024-01-24 12:43:16,354] [INFO] Target genome list was writen to GCF_000622425.1_32187_draft_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:16,370] [INFO] Task started: fastANI
[2024-01-24 12:43:16,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg01760437-aa54-44eb-83b9-06094cb35319/GCF_000622425.1_32187_draft_genomic.fna.gz --refList GCF_000622425.1_32187_draft_genomic.fna/target_genomes_gtdb.txt --output GCF_000622425.1_32187_draft_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:30,142] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:30,195] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:30,195] [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_003610455.1	s__Sulfitobacter guttiformis	99.9952	1319	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000622405.1	s__Sulfitobacter donghicola	78.0792	358	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014196805.1	s__Sulfitobacter undariae	78.0245	379	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006064855.1	s__Sulfitobacter sp006064855	77.4275	239	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.4139	255	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_000156335.1	s__Sulfitobacter sp000156335	77.3803	288	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.3666	218	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_018200035.1	s__Sulfitobacter sp018200035	77.3571	400	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	77.3236	219	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.2842	244	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.2841	264	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.284	226	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	77.2425	241	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	77.1097	247	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.0153	264	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	76.9306	259	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703405.1	s__Sulfitobacter sp002703405	76.8021	192	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_900113435.1	s__Sulfitobacter dubius	76.7618	225	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCA_003417655.1	s__Lentibacter sp003417655	76.5048	106	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	76.4278	142	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCA_013002405.1	s__Sulfitobacter sp013002405	76.3022	189	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:30,197] [INFO] GTDB search result was written to GCF_000622425.1_32187_draft_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:30,198] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:30,206] [INFO] DFAST_QC result json was written to GCF_000622425.1_32187_draft_genomic.fna/dqc_result.json
[2024-01-24 12:43:30,206] [INFO] DFAST_QC completed!
[2024-01-24 12:43:30,206] [INFO] Total running time: 0h1m24s