[2024-01-24 13:40:43,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,345] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,345] [INFO] DQC Reference Directory: /var/lib/cwl/stgf672269f-fb16-4e19-b13f-d1532652e087/dqc_reference
[2024-01-24 13:40:44,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,707] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a1c4ab0-f199-4468-b618-9d6d9a0505f9/GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/cds.fna -a GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:55,093] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:55,093] [INFO] Task started: HMMsearch
[2024-01-24 13:40:55,093] [INFO] Running command: hmmsearch --tblout GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf672269f-fb16-4e19-b13f-d1532652e087/dqc_reference/reference_markers.hmm GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:55,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:55,400] [INFO] Found 6/6 markers.
[2024-01-24 13:40:55,449] [INFO] Query marker FASTA was written to GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:55,450] [INFO] Task started: Blastn
[2024-01-24 13:40:55,450] [INFO] Running command: blastn -query GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf672269f-fb16-4e19-b13f-d1532652e087/dqc_reference/reference_markers.fasta -out GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,737] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,743] [INFO] Selected 22 target genomes.
[2024-01-24 13:40:56,743] [INFO] Target genome list was writen to GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:56,753] [INFO] Task started: fastANI
[2024-01-24 13:40:56,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a1c4ab0-f199-4468-b618-9d6d9a0505f9/GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna.gz --refList GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:16,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:16,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf672269f-fb16-4e19-b13f-d1532652e087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:16,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf672269f-fb16-4e19-b13f-d1532652e087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:16,651] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:16,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:16,652] [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
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	100.0	1149	1149	95	conclusive
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	99.9974	1146	1149	95	conclusive
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	80.2952	582	1149	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	80.1989	535	1149	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	80.095	596	1149	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	80.0517	591	1149	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	80.0401	598	1149	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.9988	527	1149	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	79.8303	546	1149	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.8115	552	1149	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.7429	511	1149	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	79.5447	474	1149	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	79.4624	518	1149	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	79.4188	524	1149	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	79.4148	519	1149	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	79.2065	461	1149	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	79.1298	467	1149	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.1211	473	1149	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	79.0407	521	1149	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	78.9917	519	1149	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.528	474	1149	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.3617	448	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:16,654] [INFO] DFAST Taxonomy check result was written to GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:16,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:16,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:16,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf672269f-fb16-4e19-b13f-d1532652e087/dqc_reference/checkm_data
[2024-01-24 13:41:16,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:16,695] [INFO] Task started: CheckM
[2024-01-24 13:41:16,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/checkm_input GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:42:15,698] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,718] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,719] [INFO] Task started: Blastn
[2024-01-24 13:42:15,719] [INFO] Running command: blastn -query GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf672269f-fb16-4e19-b13f-d1532652e087/dqc_reference/reference_markers_gtdb.fasta -out GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:17,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:17,850] [INFO] Selected 26 target genomes.
[2024-01-24 13:42:17,851] [INFO] Target genome list was writen to GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:17,902] [INFO] Task started: fastANI
[2024-01-24 13:42:17,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a1c4ab0-f199-4468-b618-9d6d9a0505f9/GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna.gz --refList GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:39,275] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:39,309] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:39,309] [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_900156695.1	s__Bieblia_A vinaykumarii	99.9974	1146	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Bieblia_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_014763785.1	s__SZUA-611 sp014763785	80.4728	508	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	80.4308	558	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_003034995.1	s__Phaeovulum veldkampii	80.3698	593	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_002358085.1	s__Thioclava arenosa	80.1807	510	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	80.0598	599	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737065.1	s__Thioclava atlantica	80.0256	556	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	79.9753	537	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_003993775.1	s__Frigidibacter sp003993775	79.9106	547	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763885.1	s__Paracoccus versutus	79.8292	547	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_001720585.1	s__Cereibacter_A johrii	79.8223	489	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCA_002423245.1	s__Frigidibacter sp002423245	79.7546	473	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCA_014763725.1	s__JACXUX01 sp014763725	79.7405	457	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACXUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	79.6243	534	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	79.5985	457	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.5859	495	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763805.1	s__Paracoccus sphaerophysae	79.5341	476	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	79.451	520	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCF_004022215.1	s__Paenirhodobacter populi	79.427	484	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
GCF_000622145.1	s__Paracoccus yeei	79.3781	521	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_002020135.1	s__Thioclava marina	79.3738	472	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.70	98.47	0.89	0.86	6	-
GCA_002841115.1	s__Albidovulum sp002841115	79.3232	488	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763905.1	s__Paracoccus halophilus	79.1771	463	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018240425.1	s__TMP-24 sp018240425	79.1274	462	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_002020355.1	s__Thioclava sediminum	79.0615	473	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
GCA_003511785.1	s__UBA7951 sp003511785	78.4856	347	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:39,311] [INFO] GTDB search result was written to GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:39,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:39,317] [INFO] DFAST_QC result json was written to GCF_900217755.1_IMG-taxon_2740891828_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:39,317] [INFO] DFAST_QC completed!
[2024-01-24 13:42:39,317] [INFO] Total running time: 0h1m56s