[2024-01-24 12:23:03,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cd3d5b9-b95a-4750-b320-47ea07c2f744/dqc_reference
[2024-01-24 12:23:04,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,696] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,697] [INFO] Running command: gunzip -c /var/lib/cwl/stg2eaf59af-d454-45ea-a1b8-09409c118031/GCF_016583505.1_ASM1658350v1_genomic.fna.gz | prodigal -d GCF_016583505.1_ASM1658350v1_genomic.fna/cds.fna -a GCF_016583505.1_ASM1658350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:16,490] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:16,491] [INFO] Task started: HMMsearch
[2024-01-24 12:23:16,491] [INFO] Running command: hmmsearch --tblout GCF_016583505.1_ASM1658350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cd3d5b9-b95a-4750-b320-47ea07c2f744/dqc_reference/reference_markers.hmm GCF_016583505.1_ASM1658350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:16,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:16,778] [INFO] Found 6/6 markers.
[2024-01-24 12:23:16,819] [INFO] Query marker FASTA was written to GCF_016583505.1_ASM1658350v1_genomic.fna/markers.fasta
[2024-01-24 12:23:16,820] [INFO] Task started: Blastn
[2024-01-24 12:23:16,820] [INFO] Running command: blastn -query GCF_016583505.1_ASM1658350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cd3d5b9-b95a-4750-b320-47ea07c2f744/dqc_reference/reference_markers.fasta -out GCF_016583505.1_ASM1658350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:17,750] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:17,754] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:17,754] [INFO] Target genome list was writen to GCF_016583505.1_ASM1658350v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:17,761] [INFO] Task started: fastANI
[2024-01-24 12:23:17,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eaf59af-d454-45ea-a1b8-09409c118031/GCF_016583505.1_ASM1658350v1_genomic.fna.gz --refList GCF_016583505.1_ASM1658350v1_genomic.fna/target_genomes.txt --output GCF_016583505.1_ASM1658350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:32,174] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:32,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cd3d5b9-b95a-4750-b320-47ea07c2f744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:32,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cd3d5b9-b95a-4750-b320-47ea07c2f744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:32,191] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:32,192] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:32,192] [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
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	100.0	1365	1366	95	conclusive
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	99.9959	1365	1366	95	conclusive
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	84.9625	929	1366	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	78.4754	421	1366	95	below_threshold
Limimonas halophila	strain=DSM 25584	GCA_900100655.1	1082479	1082479	type	True	78.248	321	1366	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.6733	410	1366	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.4811	312	1366	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	77.2819	254	1366	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.898	277	1366	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.8249	207	1366	95	below_threshold
Algihabitans albus	strain=HHTR 118	GCA_003572205.1	2164067	2164067	type	True	76.7493	195	1366	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.7204	178	1366	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.7147	150	1366	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.6359	156	1366	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.5	247	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:32,194] [INFO] DFAST Taxonomy check result was written to GCF_016583505.1_ASM1658350v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:32,194] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:32,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:32,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cd3d5b9-b95a-4750-b320-47ea07c2f744/dqc_reference/checkm_data
[2024-01-24 12:23:32,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:32,239] [INFO] Task started: CheckM
[2024-01-24 12:23:32,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583505.1_ASM1658350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583505.1_ASM1658350v1_genomic.fna/checkm_input GCF_016583505.1_ASM1658350v1_genomic.fna/checkm_result
[2024-01-24 12:24:08,183] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:08,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:08,209] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:08,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:08,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583505.1_ASM1658350v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:08,211] [INFO] Task started: Blastn
[2024-01-24 12:24:08,211] [INFO] Running command: blastn -query GCF_016583505.1_ASM1658350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cd3d5b9-b95a-4750-b320-47ea07c2f744/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583505.1_ASM1658350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:09,937] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:09,941] [INFO] Selected 13 target genomes.
[2024-01-24 12:24:09,941] [INFO] Target genome list was writen to GCF_016583505.1_ASM1658350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:09,958] [INFO] Task started: fastANI
[2024-01-24 12:24:09,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eaf59af-d454-45ea-a1b8-09409c118031/GCF_016583505.1_ASM1658350v1_genomic.fna.gz --refList GCF_016583505.1_ASM1658350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583505.1_ASM1658350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:21,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:21,723] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:21,723] [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_000515255.1	s__Rhodovibrio salinarum	99.9959	1365	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016583645.1	s__Rhodovibrio sodomensis	84.9449	930	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344765.1	s__Ferruginivarius sediminum	78.4739	420	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Ferruginivarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100655.1	s__Limimonas halophila	78.2362	322	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Limimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006969625.1	s__Algihabitans sp006969625	77.798	371	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.6986	414	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_007127165.1	s__SKZV01 sp007127165	77.6526	223	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__SKZV01	95.0	99.42	99.10	0.91	0.89	3	-
GCF_014925385.1	s__WHTV01 sp014925385	77.4908	311	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	77.3847	287	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	76.8361	206	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCA_016699855.1	s__GCA-016699855 sp016699855	76.718	230	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	76.6834	182	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869915.1	s__CAIOSQ01 sp016869915	76.4984	180	1366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	97.96	97.96	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:21,725] [INFO] GTDB search result was written to GCF_016583505.1_ASM1658350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:21,726] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:21,729] [INFO] DFAST_QC result json was written to GCF_016583505.1_ASM1658350v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:21,729] [INFO] DFAST_QC completed!
[2024-01-24 12:24:21,730] [INFO] Total running time: 0h1m18s