[2024-01-24 13:18:41,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,420] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8359da8-5531-4c6d-ad0a-efe6fa7a0519/dqc_reference
[2024-01-24 13:18:42,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,601] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,601] [INFO] Running command: gunzip -c /var/lib/cwl/stgca54214d-803e-4495-a7e0-23a40842935d/GCF_021389975.1_ASM2138997v1_genomic.fna.gz | prodigal -d GCF_021389975.1_ASM2138997v1_genomic.fna/cds.fna -a GCF_021389975.1_ASM2138997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:18,493] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:18,493] [INFO] Task started: HMMsearch
[2024-01-24 13:19:18,493] [INFO] Running command: hmmsearch --tblout GCF_021389975.1_ASM2138997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8359da8-5531-4c6d-ad0a-efe6fa7a0519/dqc_reference/reference_markers.hmm GCF_021389975.1_ASM2138997v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:18,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:18,871] [INFO] Found 6/6 markers.
[2024-01-24 13:19:18,928] [INFO] Query marker FASTA was written to GCF_021389975.1_ASM2138997v1_genomic.fna/markers.fasta
[2024-01-24 13:19:18,929] [INFO] Task started: Blastn
[2024-01-24 13:19:18,929] [INFO] Running command: blastn -query GCF_021389975.1_ASM2138997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8359da8-5531-4c6d-ad0a-efe6fa7a0519/dqc_reference/reference_markers.fasta -out GCF_021389975.1_ASM2138997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:19,514] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:19,517] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:19,517] [INFO] Target genome list was writen to GCF_021389975.1_ASM2138997v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:19,527] [INFO] Task started: fastANI
[2024-01-24 13:19:19,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgca54214d-803e-4495-a7e0-23a40842935d/GCF_021389975.1_ASM2138997v1_genomic.fna.gz --refList GCF_021389975.1_ASM2138997v1_genomic.fna/target_genomes.txt --output GCF_021389975.1_ASM2138997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:35,791] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:35,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8359da8-5531-4c6d-ad0a-efe6fa7a0519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:35,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8359da8-5531-4c6d-ad0a-efe6fa7a0519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:35,803] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:35,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:35,804] [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
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	86.0457	1428	2326	95	below_threshold
Fulvivirga marina	strain=29W222	GCA_016775155.1	2494733	2494733	type	True	81.2796	1155	2326	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	77.5602	298	2326	95	below_threshold
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	77.3671	71	2326	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	76.6969	83	2326	95	below_threshold
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	76.5655	150	2326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:35,805] [INFO] DFAST Taxonomy check result was written to GCF_021389975.1_ASM2138997v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:35,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:35,806] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:35,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8359da8-5531-4c6d-ad0a-efe6fa7a0519/dqc_reference/checkm_data
[2024-01-24 13:19:35,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:35,873] [INFO] Task started: CheckM
[2024-01-24 13:19:35,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021389975.1_ASM2138997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021389975.1_ASM2138997v1_genomic.fna/checkm_input GCF_021389975.1_ASM2138997v1_genomic.fna/checkm_result
[2024-01-24 13:21:25,286] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:25,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:25,312] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:25,313] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:25,313] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021389975.1_ASM2138997v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:25,314] [INFO] Task started: Blastn
[2024-01-24 13:21:25,314] [INFO] Running command: blastn -query GCF_021389975.1_ASM2138997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8359da8-5531-4c6d-ad0a-efe6fa7a0519/dqc_reference/reference_markers_gtdb.fasta -out GCF_021389975.1_ASM2138997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:26,104] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:26,111] [INFO] Selected 20 target genomes.
[2024-01-24 13:21:26,111] [INFO] Target genome list was writen to GCF_021389975.1_ASM2138997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:26,178] [INFO] Task started: fastANI
[2024-01-24 13:21:26,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgca54214d-803e-4495-a7e0-23a40842935d/GCF_021389975.1_ASM2138997v1_genomic.fna.gz --refList GCF_021389975.1_ASM2138997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021389975.1_ASM2138997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:42,320] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:42,334] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:21:42,334] [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_009711405.1	s__Fulvivirga kasyanovii	86.0536	1426	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775155.1	s__Fulvivirga sp016775155	81.2755	1157	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331535.1	s__Fulvivirga imtechensis	77.5602	298	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017068455.1	s__Fulvivirga sp017068455	77.3671	71	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097395.1	s__Fulvivirga sp007097395	76.9507	85	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711475.1	s__Fulvivirga aurantia	76.6969	83	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757215.1	s__Fulvivirga sp016757215	76.5803	149	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657315.1	s__Fulvivirga sp001657315	76.2992	71	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338655.1	s__Fulvivirga sp002338655	76.1199	84	2326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:42,336] [INFO] GTDB search result was written to GCF_021389975.1_ASM2138997v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:42,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:42,339] [INFO] DFAST_QC result json was written to GCF_021389975.1_ASM2138997v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:42,339] [INFO] DFAST_QC completed!
[2024-01-24 13:21:42,340] [INFO] Total running time: 0h3m1s