[2024-01-24 12:53:57,065] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:57,067] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:57,068] [INFO] DQC Reference Directory: /var/lib/cwl/stgae245895-fa99-440d-b5cc-210ae64c98d1/dqc_reference
[2024-01-24 12:53:58,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,488] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1992d3c-f7a6-4b43-a3f8-841b61015103/GCF_031454095.1_ASM3145409v1_genomic.fna.gz | prodigal -d GCF_031454095.1_ASM3145409v1_genomic.fna/cds.fna -a GCF_031454095.1_ASM3145409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:31,903] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:31,903] [INFO] Task started: HMMsearch
[2024-01-24 12:54:31,903] [INFO] Running command: hmmsearch --tblout GCF_031454095.1_ASM3145409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae245895-fa99-440d-b5cc-210ae64c98d1/dqc_reference/reference_markers.hmm GCF_031454095.1_ASM3145409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:32,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:32,257] [INFO] Found 6/6 markers.
[2024-01-24 12:54:32,318] [INFO] Query marker FASTA was written to GCF_031454095.1_ASM3145409v1_genomic.fna/markers.fasta
[2024-01-24 12:54:32,318] [INFO] Task started: Blastn
[2024-01-24 12:54:32,318] [INFO] Running command: blastn -query GCF_031454095.1_ASM3145409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae245895-fa99-440d-b5cc-210ae64c98d1/dqc_reference/reference_markers.fasta -out GCF_031454095.1_ASM3145409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:32,911] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:32,914] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:32,915] [INFO] Target genome list was writen to GCF_031454095.1_ASM3145409v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:32,927] [INFO] Task started: fastANI
[2024-01-24 12:54:32,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1992d3c-f7a6-4b43-a3f8-841b61015103/GCF_031454095.1_ASM3145409v1_genomic.fna.gz --refList GCF_031454095.1_ASM3145409v1_genomic.fna/target_genomes.txt --output GCF_031454095.1_ASM3145409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:46,073] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:46,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae245895-fa99-440d-b5cc-210ae64c98d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:46,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae245895-fa99-440d-b5cc-210ae64c98d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:46,083] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:46,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:46,083] [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
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	99.9992	2461	2469	95	conclusive
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	79.7429	919	2469	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	79.7252	931	2469	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	77.2736	279	2469	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	77.0915	319	2469	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.0792	122	2469	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.0506	102	2469	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	75.9565	115	2469	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	75.8971	81	2469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:46,085] [INFO] DFAST Taxonomy check result was written to GCF_031454095.1_ASM3145409v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:46,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:46,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:46,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae245895-fa99-440d-b5cc-210ae64c98d1/dqc_reference/checkm_data
[2024-01-24 12:54:46,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:46,150] [INFO] Task started: CheckM
[2024-01-24 12:54:46,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031454095.1_ASM3145409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031454095.1_ASM3145409v1_genomic.fna/checkm_input GCF_031454095.1_ASM3145409v1_genomic.fna/checkm_result
[2024-01-24 12:56:11,451] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:11,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:11,479] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:11,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:11,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031454095.1_ASM3145409v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:11,480] [INFO] Task started: Blastn
[2024-01-24 12:56:11,480] [INFO] Running command: blastn -query GCF_031454095.1_ASM3145409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae245895-fa99-440d-b5cc-210ae64c98d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_031454095.1_ASM3145409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:12,211] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:12,214] [INFO] Selected 10 target genomes.
[2024-01-24 12:56:12,214] [INFO] Target genome list was writen to GCF_031454095.1_ASM3145409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:12,224] [INFO] Task started: fastANI
[2024-01-24 12:56:12,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1992d3c-f7a6-4b43-a3f8-841b61015103/GCF_031454095.1_ASM3145409v1_genomic.fna.gz --refList GCF_031454095.1_ASM3145409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031454095.1_ASM3145409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:22,867] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:22,874] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:22,874] [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_014641615.1	s__Filimonas zeae	99.9992	2461	2469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007994055.1	s__Filimonas endophytica	84.1909	1555	2469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097095.1	s__Filimonas sp003097095	81.3899	1306	2469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355595.1	s__Filimonas lacunae	79.7261	930	2469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004118675.1	s__Filimonas effusa	77.2751	278	2469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412455.1	s__Deminuibacter soli	77.1179	317	2469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	76.6735	173	2469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:22,877] [INFO] GTDB search result was written to GCF_031454095.1_ASM3145409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:22,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:22,880] [INFO] DFAST_QC result json was written to GCF_031454095.1_ASM3145409v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:22,880] [INFO] DFAST_QC completed!
[2024-01-24 12:56:22,880] [INFO] Total running time: 0h2m26s