[2024-01-24 13:18:46,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg876ff50a-4893-4969-b6db-db5355aff7ce/dqc_reference
[2024-01-24 13:18:47,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,951] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc2e77f3-2a2a-4d0c-9b9f-97d625eee272/GCF_014651615.1_ASM1465161v1_genomic.fna.gz | prodigal -d GCF_014651615.1_ASM1465161v1_genomic.fna/cds.fna -a GCF_014651615.1_ASM1465161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:21,169] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:21,170] [INFO] Task started: HMMsearch
[2024-01-24 13:19:21,170] [INFO] Running command: hmmsearch --tblout GCF_014651615.1_ASM1465161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg876ff50a-4893-4969-b6db-db5355aff7ce/dqc_reference/reference_markers.hmm GCF_014651615.1_ASM1465161v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:21,478] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:21,479] [INFO] Found 6/6 markers.
[2024-01-24 13:19:21,531] [INFO] Query marker FASTA was written to GCF_014651615.1_ASM1465161v1_genomic.fna/markers.fasta
[2024-01-24 13:19:21,532] [INFO] Task started: Blastn
[2024-01-24 13:19:21,532] [INFO] Running command: blastn -query GCF_014651615.1_ASM1465161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876ff50a-4893-4969-b6db-db5355aff7ce/dqc_reference/reference_markers.fasta -out GCF_014651615.1_ASM1465161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:22,140] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:22,144] [INFO] Selected 25 target genomes.
[2024-01-24 13:19:22,144] [INFO] Target genome list was writen to GCF_014651615.1_ASM1465161v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:22,175] [INFO] Task started: fastANI
[2024-01-24 13:19:22,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2e77f3-2a2a-4d0c-9b9f-97d625eee272/GCF_014651615.1_ASM1465161v1_genomic.fna.gz --refList GCF_014651615.1_ASM1465161v1_genomic.fna/target_genomes.txt --output GCF_014651615.1_ASM1465161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:47,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg876ff50a-4893-4969-b6db-db5355aff7ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:47,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg876ff50a-4893-4969-b6db-db5355aff7ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:47,599] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:47,599] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:47,599] [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
Persicitalea jodogahamensis	strain=KCTC 12866	GCA_014651615.1	402147	402147	type	True	100.0	2128	2128	95	conclusive
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	75.7547	104	2128	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	75.6644	109	2128	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	75.6296	58	2128	95	below_threshold
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	75.4684	115	2128	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	75.4589	52	2128	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	75.452	91	2128	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	75.4497	72	2128	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	75.3857	68	2128	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	75.364	50	2128	95	below_threshold
Runella aurantiaca	strain=YX9	GCA_003339505.1	2282308	2282308	type	True	75.3046	64	2128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,602] [INFO] DFAST Taxonomy check result was written to GCF_014651615.1_ASM1465161v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:47,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:47,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:47,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg876ff50a-4893-4969-b6db-db5355aff7ce/dqc_reference/checkm_data
[2024-01-24 13:19:47,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:47,665] [INFO] Task started: CheckM
[2024-01-24 13:19:47,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651615.1_ASM1465161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651615.1_ASM1465161v1_genomic.fna/checkm_input GCF_014651615.1_ASM1465161v1_genomic.fna/checkm_result
[2024-01-24 13:21:14,404] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:14,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:14,426] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:14,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:14,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651615.1_ASM1465161v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:14,427] [INFO] Task started: Blastn
[2024-01-24 13:21:14,427] [INFO] Running command: blastn -query GCF_014651615.1_ASM1465161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876ff50a-4893-4969-b6db-db5355aff7ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651615.1_ASM1465161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:15,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:15,148] [INFO] Selected 25 target genomes.
[2024-01-24 13:21:15,148] [INFO] Target genome list was writen to GCF_014651615.1_ASM1465161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:15,217] [INFO] Task started: fastANI
[2024-01-24 13:21:15,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2e77f3-2a2a-4d0c-9b9f-97d625eee272/GCF_014651615.1_ASM1465161v1_genomic.fna.gz --refList GCF_014651615.1_ASM1465161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651615.1_ASM1465161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:39,528] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:39,539] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:39,540] [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_014651615.1	s__Persicitalea jodogahamensis	100.0	2128	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Persicitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009296315.1	s__Persicitalea sp009296315	78.5828	609	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Persicitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165045.1	s__Dyadobacter sp907165045	75.9481	63	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641595.1	s__Dyadobacter endophyticus	75.7547	104	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382205.1	s__Dyadobacter beijingensis	75.7051	121	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109045.1	s__Dyadobacter sp900109045	75.6963	97	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	75.6644	109	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149045.1	s__Dyadobacter flavalbus	75.6296	58	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	75.4922	50	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014695.1	s__Dyadobacter jiangsuensis	75.4684	115	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230225.1	s__Spirosoma fluviale	75.3723	69	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339505.1	s__Runella sp003339505	75.3046	64	2128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:39,542] [INFO] GTDB search result was written to GCF_014651615.1_ASM1465161v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:39,542] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:39,545] [INFO] DFAST_QC result json was written to GCF_014651615.1_ASM1465161v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:39,545] [INFO] DFAST_QC completed!
[2024-01-24 13:21:39,545] [INFO] Total running time: 0h2m53s