[2024-01-24 15:26:47,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:47,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:47,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg953a8975-9c5e-4b23-b724-808ef436aea7/dqc_reference
[2024-01-24 15:26:48,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:48,876] [INFO] Task started: Prodigal
[2024-01-24 15:26:48,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c04711e-9d7a-4126-bf39-97a0bd8eef75/GCF_000934545.1_ASM93454v1_genomic.fna.gz | prodigal -d GCF_000934545.1_ASM93454v1_genomic.fna/cds.fna -a GCF_000934545.1_ASM93454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:58,652] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:58,652] [INFO] Task started: HMMsearch
[2024-01-24 15:26:58,653] [INFO] Running command: hmmsearch --tblout GCF_000934545.1_ASM93454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg953a8975-9c5e-4b23-b724-808ef436aea7/dqc_reference/reference_markers.hmm GCF_000934545.1_ASM93454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:58,934] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:58,935] [INFO] Found 6/6 markers.
[2024-01-24 15:26:58,962] [INFO] Query marker FASTA was written to GCF_000934545.1_ASM93454v1_genomic.fna/markers.fasta
[2024-01-24 15:26:58,963] [INFO] Task started: Blastn
[2024-01-24 15:26:58,963] [INFO] Running command: blastn -query GCF_000934545.1_ASM93454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg953a8975-9c5e-4b23-b724-808ef436aea7/dqc_reference/reference_markers.fasta -out GCF_000934545.1_ASM93454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:59,553] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:59,557] [INFO] Selected 30 target genomes.
[2024-01-24 15:26:59,557] [INFO] Target genome list was writen to GCF_000934545.1_ASM93454v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:59,571] [INFO] Task started: fastANI
[2024-01-24 15:26:59,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c04711e-9d7a-4126-bf39-97a0bd8eef75/GCF_000934545.1_ASM93454v1_genomic.fna.gz --refList GCF_000934545.1_ASM93454v1_genomic.fna/target_genomes.txt --output GCF_000934545.1_ASM93454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:20,014] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:20,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg953a8975-9c5e-4b23-b724-808ef436aea7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:20,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg953a8975-9c5e-4b23-b724-808ef436aea7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:20,022] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:20,022] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:20,022] [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
Rugosibacter aromaticivorans	strain=Ca6	GCA_000934545.1	1565605	1565605	type	True	100.0	977	978	95	conclusive
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	78.3298	101	978	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	77.8632	97	978	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.3795	70	978	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.6792	79	978	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.6725	64	978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:20,023] [INFO] DFAST Taxonomy check result was written to GCF_000934545.1_ASM93454v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:20,024] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:20,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:20,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg953a8975-9c5e-4b23-b724-808ef436aea7/dqc_reference/checkm_data
[2024-01-24 15:27:20,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:20,061] [INFO] Task started: CheckM
[2024-01-24 15:27:20,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000934545.1_ASM93454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000934545.1_ASM93454v1_genomic.fna/checkm_input GCF_000934545.1_ASM93454v1_genomic.fna/checkm_result
[2024-01-24 15:27:53,989] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:53,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:54,010] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:54,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:54,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000934545.1_ASM93454v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:54,012] [INFO] Task started: Blastn
[2024-01-24 15:27:54,012] [INFO] Running command: blastn -query GCF_000934545.1_ASM93454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg953a8975-9c5e-4b23-b724-808ef436aea7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000934545.1_ASM93454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:54,871] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:54,874] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:54,875] [INFO] Target genome list was writen to GCF_000934545.1_ASM93454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:54,901] [INFO] Task started: fastANI
[2024-01-24 15:27:54,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c04711e-9d7a-4126-bf39-97a0bd8eef75/GCF_000934545.1_ASM93454v1_genomic.fna.gz --refList GCF_000934545.1_ASM93454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000934545.1_ASM93454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:03,728] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:03,750] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:03,751] [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_000934545.1	s__Rugosibacter aromaticivorans	100.0	978	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	99.39	99.39	0.96	0.96	2	conclusive
GCA_004322535.1	s__Rugosibacter sp004322535	86.1627	624	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620215.1	s__Rugosibacter sp011620215	85.2336	505	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422995.1	s__Rugosibacter sp002422995	79.2308	209	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	97.21	96.23	0.74	0.65	4	-
GCA_002424865.1	s__Rugosibacter sp002424865	79.1013	368	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	99.77	99.73	0.92	0.91	4	-
GCA_016235025.1	s__Rugosibacter sp016235025	78.3402	235	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828635.1	s__Sulfuritalea hydrogenivorans	77.8811	149	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842395.1	s__Rugosibacter sp002842395	77.3767	174	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828935.1	s__Sulfuritalea sp001828935	76.9152	140	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848955.1	s__Sulfuritalea sp903848955	76.8701	133	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.61	99.42	0.91	0.84	24	-
GCA_016702335.1	s__JADJEF01 sp016702335	76.7854	86	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JADJEF01	95.0	99.13	99.13	0.90	0.90	2	-
GCA_903946745.1	s__CAJAWW01 sp903946745	76.7116	113	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAJAWW01	95.0	99.25	99.21	0.88	0.87	4	-
GCA_012026675.1	s__Sulfuritalea sp012026675	76.5392	118	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825305.1	s__Sulfurisoma sp018825305	76.0128	88	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:03,753] [INFO] GTDB search result was written to GCF_000934545.1_ASM93454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:03,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:03,758] [INFO] DFAST_QC result json was written to GCF_000934545.1_ASM93454v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:03,758] [INFO] DFAST_QC completed!
[2024-01-24 15:28:03,758] [INFO] Total running time: 0h1m16s