[2024-01-24 11:22:49,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,039] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg523ce322-fcf6-4915-a23f-2da73f20842f/dqc_reference
[2024-01-24 11:22:50,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,268] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg21fe2fc4-e05e-4d61-bed6-766f31e8428d/GCF_004340665.1_ASM434066v1_genomic.fna.gz | prodigal -d GCF_004340665.1_ASM434066v1_genomic.fna/cds.fna -a GCF_004340665.1_ASM434066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:09,197] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:09,197] [INFO] Task started: HMMsearch
[2024-01-24 11:23:09,198] [INFO] Running command: hmmsearch --tblout GCF_004340665.1_ASM434066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg523ce322-fcf6-4915-a23f-2da73f20842f/dqc_reference/reference_markers.hmm GCF_004340665.1_ASM434066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:09,506] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:09,512] [INFO] Found 6/6 markers.
[2024-01-24 11:23:09,558] [INFO] Query marker FASTA was written to GCF_004340665.1_ASM434066v1_genomic.fna/markers.fasta
[2024-01-24 11:23:09,559] [INFO] Task started: Blastn
[2024-01-24 11:23:09,559] [INFO] Running command: blastn -query GCF_004340665.1_ASM434066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg523ce322-fcf6-4915-a23f-2da73f20842f/dqc_reference/reference_markers.fasta -out GCF_004340665.1_ASM434066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:10,177] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:10,183] [INFO] Selected 19 target genomes.
[2024-01-24 11:23:10,184] [INFO] Target genome list was writen to GCF_004340665.1_ASM434066v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:10,192] [INFO] Task started: fastANI
[2024-01-24 11:23:10,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg21fe2fc4-e05e-4d61-bed6-766f31e8428d/GCF_004340665.1_ASM434066v1_genomic.fna.gz --refList GCF_004340665.1_ASM434066v1_genomic.fna/target_genomes.txt --output GCF_004340665.1_ASM434066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:30,066] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:30,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg523ce322-fcf6-4915-a23f-2da73f20842f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:30,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg523ce322-fcf6-4915-a23f-2da73f20842f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:30,082] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:23:30,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:30,083] [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
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	100.0	1719	1719	95	conclusive
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	99.9992	1717	1719	95	conclusive
Pedobacter petrophilus	strain=LMG 29686	GCA_009674725.1	1908241	1908241	type	True	81.5436	1004	1719	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	80.3326	651	1719	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	80.2021	753	1719	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	80.1886	753	1719	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	80.1534	733	1719	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.1445	649	1719	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	80.1158	714	1719	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	80.0335	696	1719	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.9765	636	1719	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	79.9577	731	1719	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	79.9118	658	1719	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	79.8127	584	1719	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	79.7748	701	1719	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	79.7083	734	1719	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	79.0567	602	1719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:30,085] [INFO] DFAST Taxonomy check result was written to GCF_004340665.1_ASM434066v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:30,086] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:30,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:30,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg523ce322-fcf6-4915-a23f-2da73f20842f/dqc_reference/checkm_data
[2024-01-24 11:23:30,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:30,138] [INFO] Task started: CheckM
[2024-01-24 11:23:30,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340665.1_ASM434066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340665.1_ASM434066v1_genomic.fna/checkm_input GCF_004340665.1_ASM434066v1_genomic.fna/checkm_result
[2024-01-24 11:24:25,709] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:25,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:25,732] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:25,733] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:25,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340665.1_ASM434066v1_genomic.fna/markers.fasta)
[2024-01-24 11:24:25,733] [INFO] Task started: Blastn
[2024-01-24 11:24:25,733] [INFO] Running command: blastn -query GCF_004340665.1_ASM434066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg523ce322-fcf6-4915-a23f-2da73f20842f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340665.1_ASM434066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:26,559] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:26,563] [INFO] Selected 12 target genomes.
[2024-01-24 11:24:26,564] [INFO] Target genome list was writen to GCF_004340665.1_ASM434066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:26,584] [INFO] Task started: fastANI
[2024-01-24 11:24:26,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg21fe2fc4-e05e-4d61-bed6-766f31e8428d/GCF_004340665.1_ASM434066v1_genomic.fna.gz --refList GCF_004340665.1_ASM434066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340665.1_ASM434066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:41,422] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:41,446] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:41,447] [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_004340665.1	s__Pedobacter psychrotolerans	100.0	1719	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000708265.2	s__Pedobacter sp000708265	90.3222	1414	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197755.1	s__Pedobacter sp002197755	84.5968	1225	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674725.1	s__Pedobacter petrophilus	81.5622	1001	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258495.1	s__Pedobacter agri	80.341	650	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_004331735.1	s__Pedobacter sp004331735	80.1419	735	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339865.1	s__Pedobacter chinensis	80.1342	711	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342125.1	s__Pedobacter sp004342125	80.1164	761	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_003387415.1	s__Pedobacter sp003387415	80.0637	724	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331675.1	s__Pedobacter sp004331675	80.0417	695	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100705.1	s__Pedobacter terrae	79.7672	702	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423945.1	s__Pedobacter sp001423945	79.449	546	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:41,449] [INFO] GTDB search result was written to GCF_004340665.1_ASM434066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:41,449] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:41,453] [INFO] DFAST_QC result json was written to GCF_004340665.1_ASM434066v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:41,453] [INFO] DFAST_QC completed!
[2024-01-24 11:24:41,453] [INFO] Total running time: 0h1m52s