[2024-01-24 12:36:54,757] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:54,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:54,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f25280d-69fe-40f0-8c6c-bda528052147/dqc_reference
[2024-01-24 12:36:57,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:57,081] [INFO] Task started: Prodigal
[2024-01-24 12:36:57,082] [INFO] Running command: gunzip -c /var/lib/cwl/stg5af9ee02-d3b4-456a-9976-2623a02cc941/GCF_022570735.2_ASM2257073v2_genomic.fna.gz | prodigal -d GCF_022570735.2_ASM2257073v2_genomic.fna/cds.fna -a GCF_022570735.2_ASM2257073v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:12,596] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:12,597] [INFO] Task started: HMMsearch
[2024-01-24 12:37:12,597] [INFO] Running command: hmmsearch --tblout GCF_022570735.2_ASM2257073v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f25280d-69fe-40f0-8c6c-bda528052147/dqc_reference/reference_markers.hmm GCF_022570735.2_ASM2257073v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:12,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:12,988] [INFO] Found 6/6 markers.
[2024-01-24 12:37:13,036] [INFO] Query marker FASTA was written to GCF_022570735.2_ASM2257073v2_genomic.fna/markers.fasta
[2024-01-24 12:37:13,037] [INFO] Task started: Blastn
[2024-01-24 12:37:13,037] [INFO] Running command: blastn -query GCF_022570735.2_ASM2257073v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f25280d-69fe-40f0-8c6c-bda528052147/dqc_reference/reference_markers.fasta -out GCF_022570735.2_ASM2257073v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:13,764] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:13,767] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:13,767] [INFO] Target genome list was writen to GCF_022570735.2_ASM2257073v2_genomic.fna/target_genomes.txt
[2024-01-24 12:37:13,778] [INFO] Task started: fastANI
[2024-01-24 12:37:13,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af9ee02-d3b4-456a-9976-2623a02cc941/GCF_022570735.2_ASM2257073v2_genomic.fna.gz --refList GCF_022570735.2_ASM2257073v2_genomic.fna/target_genomes.txt --output GCF_022570735.2_ASM2257073v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:22,552] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:22,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f25280d-69fe-40f0-8c6c-bda528052147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:22,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f25280d-69fe-40f0-8c6c-bda528052147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:22,565] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:22,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:22,566] [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
Gramella flava	strain=JLT2011	GCA_001951155.1	1486245	1486245	type	True	79.6643	370	1248	95	below_threshold
Gramella flava	strain=JLT2011	GCA_002120265.1	1486245	1486245	type	True	79.4994	367	1248	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	79.4606	440	1248	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	79.4317	438	1248	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	79.4091	454	1248	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	79.2296	508	1248	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	79.209	508	1248	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	79.1909	442	1248	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	79.1515	395	1248	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	79.015	463	1248	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	78.7198	334	1248	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	76.7174	73	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:22,571] [INFO] DFAST Taxonomy check result was written to GCF_022570735.2_ASM2257073v2_genomic.fna/tc_result.tsv
[2024-01-24 12:37:22,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:22,573] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:22,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f25280d-69fe-40f0-8c6c-bda528052147/dqc_reference/checkm_data
[2024-01-24 12:37:22,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:22,618] [INFO] Task started: CheckM
[2024-01-24 12:37:22,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022570735.2_ASM2257073v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022570735.2_ASM2257073v2_genomic.fna/checkm_input GCF_022570735.2_ASM2257073v2_genomic.fna/checkm_result
[2024-01-24 12:38:09,738] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:09,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:09,763] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:09,763] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:09,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022570735.2_ASM2257073v2_genomic.fna/markers.fasta)
[2024-01-24 12:38:09,764] [INFO] Task started: Blastn
[2024-01-24 12:38:09,764] [INFO] Running command: blastn -query GCF_022570735.2_ASM2257073v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f25280d-69fe-40f0-8c6c-bda528052147/dqc_reference/reference_markers_gtdb.fasta -out GCF_022570735.2_ASM2257073v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:10,600] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:10,604] [INFO] Selected 11 target genomes.
[2024-01-24 12:38:10,605] [INFO] Target genome list was writen to GCF_022570735.2_ASM2257073v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:10,616] [INFO] Task started: fastANI
[2024-01-24 12:38:10,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af9ee02-d3b4-456a-9976-2623a02cc941/GCF_022570735.2_ASM2257073v2_genomic.fna.gz --refList GCF_022570735.2_ASM2257073v2_genomic.fna/target_genomes_gtdb.txt --output GCF_022570735.2_ASM2257073v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:18,443] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:18,456] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:38:18,456] [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_009735695.1	s__Gramella sp009735695	84.1534	931	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001951155.1	s__Gramella flava	79.6618	371	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	99.04	98.07	0.94	0.88	3	-
GCF_000060345.1	s__Gramella forsetii	79.4362	438	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003054225.1	s__Gramella gaetbulicola	79.2296	508	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	79.2184	507	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	79.1904	442	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_007050985.1	s__Gramella sabulilitoris	79.1401	396	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004332155.1	s__Gramella sp004332155	79.028	448	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889005.1	s__Gramella salexigens	78.7198	334	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006714895.1	s__Gramella sp006714895	78.4991	331	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	77.3414	204	1248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:18,457] [INFO] GTDB search result was written to GCF_022570735.2_ASM2257073v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:18,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:18,462] [INFO] DFAST_QC result json was written to GCF_022570735.2_ASM2257073v2_genomic.fna/dqc_result.json
[2024-01-24 12:38:18,462] [INFO] DFAST_QC completed!
[2024-01-24 12:38:18,462] [INFO] Total running time: 0h1m24s