[2024-01-24 11:12:36,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,242] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bbf9093-bf10-4b22-b897-0ca272cc3a53/dqc_reference
[2024-01-24 11:12:38,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,664] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,664] [INFO] Running command: gunzip -c /var/lib/cwl/stgc403b14f-88ec-4a9f-985e-6daec06b103c/GCF_028294535.1_ASM2829453v1_genomic.fna.gz | prodigal -d GCF_028294535.1_ASM2829453v1_genomic.fna/cds.fna -a GCF_028294535.1_ASM2829453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:51,457] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:51,457] [INFO] Task started: HMMsearch
[2024-01-24 11:12:51,458] [INFO] Running command: hmmsearch --tblout GCF_028294535.1_ASM2829453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bbf9093-bf10-4b22-b897-0ca272cc3a53/dqc_reference/reference_markers.hmm GCF_028294535.1_ASM2829453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:51,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:51,661] [INFO] Found 6/6 markers.
[2024-01-24 11:12:51,697] [INFO] Query marker FASTA was written to GCF_028294535.1_ASM2829453v1_genomic.fna/markers.fasta
[2024-01-24 11:12:51,697] [INFO] Task started: Blastn
[2024-01-24 11:12:51,698] [INFO] Running command: blastn -query GCF_028294535.1_ASM2829453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bbf9093-bf10-4b22-b897-0ca272cc3a53/dqc_reference/reference_markers.fasta -out GCF_028294535.1_ASM2829453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:52,504] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:52,507] [INFO] Selected 20 target genomes.
[2024-01-24 11:12:52,507] [INFO] Target genome list was writen to GCF_028294535.1_ASM2829453v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:52,527] [INFO] Task started: fastANI
[2024-01-24 11:12:52,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgc403b14f-88ec-4a9f-985e-6daec06b103c/GCF_028294535.1_ASM2829453v1_genomic.fna.gz --refList GCF_028294535.1_ASM2829453v1_genomic.fna/target_genomes.txt --output GCF_028294535.1_ASM2829453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:06,069] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:06,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bbf9093-bf10-4b22-b897-0ca272cc3a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:06,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bbf9093-bf10-4b22-b897-0ca272cc3a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:06,084] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:06,085] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:06,085] [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
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	82.9776	630	1325	95	below_threshold
Paracoccus seriniphilus	strain=DSM 14827	GCA_900199195.1	184748	184748	type	True	81.5927	820	1325	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	79.6098	481	1325	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.5869	517	1325	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.5617	431	1325	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	79.4971	530	1325	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	79.497	505	1325	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.4102	476	1325	95	below_threshold
Paracoccus amoyensis	strain=11-3	GCA_014490725.1	2760093	2760093	type	True	79.3718	441	1325	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	79.3691	468	1325	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	79.3315	441	1325	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	79.1885	455	1325	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	79.1572	461	1325	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.0233	422	1325	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	78.9898	467	1325	95	below_threshold
Paracoccus subflavus	strain=GY0581	GCA_004310345.1	2528244	2528244	type	True	78.9733	420	1325	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	78.8345	401	1325	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	78.8071	453	1325	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	78.7819	400	1325	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	78.7705	462	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:06,086] [INFO] DFAST Taxonomy check result was written to GCF_028294535.1_ASM2829453v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:06,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:06,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:06,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bbf9093-bf10-4b22-b897-0ca272cc3a53/dqc_reference/checkm_data
[2024-01-24 11:13:06,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:06,128] [INFO] Task started: CheckM
[2024-01-24 11:13:06,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028294535.1_ASM2829453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028294535.1_ASM2829453v1_genomic.fna/checkm_input GCF_028294535.1_ASM2829453v1_genomic.fna/checkm_result
[2024-01-24 11:13:49,153] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:49,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:49,172] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:49,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:49,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028294535.1_ASM2829453v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:49,173] [INFO] Task started: Blastn
[2024-01-24 11:13:49,173] [INFO] Running command: blastn -query GCF_028294535.1_ASM2829453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bbf9093-bf10-4b22-b897-0ca272cc3a53/dqc_reference/reference_markers_gtdb.fasta -out GCF_028294535.1_ASM2829453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:50,584] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:50,591] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:50,592] [INFO] Target genome list was writen to GCF_028294535.1_ASM2829453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:50,604] [INFO] Task started: fastANI
[2024-01-24 11:13:50,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgc403b14f-88ec-4a9f-985e-6daec06b103c/GCF_028294535.1_ASM2829453v1_genomic.fna.gz --refList GCF_028294535.1_ASM2829453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028294535.1_ASM2829453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:01,332] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:01,344] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:01,344] [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_900111675.1	s__Paracoccus homiensis	82.9676	631	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199195.1	s__Paracoccus seriniphilus	81.5754	822	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	80.1987	557	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_018860165.1	s__Paracoccus sp018860165	80.0749	576	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860625.1	s__Paracoccus sp018860625	79.8987	444	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002294185.1	s__Paracoccus sp002294185	79.5985	472	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
GCF_900110285.1	s__Paracoccus alcaliphilus	79.5918	480	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	79.5019	529	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900631945.1	s__Paracoccus haematequi	79.3836	462	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259195.1	s__Paracoccus sediminilitoris	79.3493	470	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
GCF_016629665.1	s__Paracoccus caeni	79.2987	444	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	79.1675	457	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_003697785.1	s__Paracoccus alkanivorans	79.1667	495	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310345.1	s__Paracoccus subflavus	78.9794	420	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188295.1	s__Paracoccus sediminis	78.7794	463	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:01,346] [INFO] GTDB search result was written to GCF_028294535.1_ASM2829453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:01,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:01,350] [INFO] DFAST_QC result json was written to GCF_028294535.1_ASM2829453v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:01,350] [INFO] DFAST_QC completed!
[2024-01-24 11:14:01,350] [INFO] Total running time: 0h1m25s