[2024-01-24 15:26:54,358] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,381] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2741ad5-771a-4dcc-aaa0-d1f8e7b4f581/dqc_reference
[2024-01-24 15:26:55,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:55,692] [INFO] Task started: Prodigal
[2024-01-24 15:26:55,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgc823f0df-80c8-4815-993b-eebc51c92da8/GCF_004331735.1_ASM433173v1_genomic.fna.gz | prodigal -d GCF_004331735.1_ASM433173v1_genomic.fna/cds.fna -a GCF_004331735.1_ASM433173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:17,764] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:17,765] [INFO] Task started: HMMsearch
[2024-01-24 15:27:17,765] [INFO] Running command: hmmsearch --tblout GCF_004331735.1_ASM433173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2741ad5-771a-4dcc-aaa0-d1f8e7b4f581/dqc_reference/reference_markers.hmm GCF_004331735.1_ASM433173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:18,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:18,140] [INFO] Found 6/6 markers.
[2024-01-24 15:27:18,206] [INFO] Query marker FASTA was written to GCF_004331735.1_ASM433173v1_genomic.fna/markers.fasta
[2024-01-24 15:27:18,207] [INFO] Task started: Blastn
[2024-01-24 15:27:18,207] [INFO] Running command: blastn -query GCF_004331735.1_ASM433173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2741ad5-771a-4dcc-aaa0-d1f8e7b4f581/dqc_reference/reference_markers.fasta -out GCF_004331735.1_ASM433173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:18,831] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:18,834] [INFO] Selected 12 target genomes.
[2024-01-24 15:27:18,834] [INFO] Target genome list was writen to GCF_004331735.1_ASM433173v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:18,839] [INFO] Task started: fastANI
[2024-01-24 15:27:18,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgc823f0df-80c8-4815-993b-eebc51c92da8/GCF_004331735.1_ASM433173v1_genomic.fna.gz --refList GCF_004331735.1_ASM433173v1_genomic.fna/target_genomes.txt --output GCF_004331735.1_ASM433173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:35,199] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:35,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2741ad5-771a-4dcc-aaa0-d1f8e7b4f581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:35,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2741ad5-771a-4dcc-aaa0-d1f8e7b4f581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:35,211] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:35,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:35,211] [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 psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	100.0	2001	2003	95	conclusive
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	89.1663	1391	2003	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	89.0688	1413	2003	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	88.9604	1212	2003	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	86.0038	1251	2003	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	86.0033	1268	2003	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	82.7517	1172	2003	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	81.4739	1080	2003	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	80.4934	780	2003	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	79.4329	626	2003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:35,213] [INFO] DFAST Taxonomy check result was written to GCF_004331735.1_ASM433173v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:35,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:35,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:35,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2741ad5-771a-4dcc-aaa0-d1f8e7b4f581/dqc_reference/checkm_data
[2024-01-24 15:27:35,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:35,279] [INFO] Task started: CheckM
[2024-01-24 15:27:35,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331735.1_ASM433173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331735.1_ASM433173v1_genomic.fna/checkm_input GCF_004331735.1_ASM433173v1_genomic.fna/checkm_result
[2024-01-24 15:28:35,332] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:35,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:35,364] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:35,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:35,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331735.1_ASM433173v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:35,364] [INFO] Task started: Blastn
[2024-01-24 15:28:35,365] [INFO] Running command: blastn -query GCF_004331735.1_ASM433173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2741ad5-771a-4dcc-aaa0-d1f8e7b4f581/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331735.1_ASM433173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:36,171] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:36,174] [INFO] Selected 12 target genomes.
[2024-01-24 15:28:36,174] [INFO] Target genome list was writen to GCF_004331735.1_ASM433173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:36,182] [INFO] Task started: fastANI
[2024-01-24 15:28:36,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgc823f0df-80c8-4815-993b-eebc51c92da8/GCF_004331735.1_ASM433173v1_genomic.fna.gz --refList GCF_004331735.1_ASM433173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331735.1_ASM433173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:53,901] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:53,911] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:53,911] [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_004331735.1	s__Pedobacter sp004331735	100.0	2001	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004310665.1	s__Pedobacter kyonggii	89.1769	1390	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	89.0895	1411	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	89.01	1432	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708285.2	s__Pedobacter borealis	88.9366	1214	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613605.1	s__Pedobacter sp018613605	88.7714	1403	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_003054145.1	s__Pedobacter sp003054145	88.6167	1410	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387415.1	s__Pedobacter sp003387415	88.534	1352	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692875.1	s__Pedobacter sp011759615	87.5392	1367	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_014205835.1	s__Pedobacter sp014205835	87.153	1334	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664035.1	s__Pedobacter alluvionis	85.9909	1269	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004342125.1	s__Pedobacter sp004342125	85.891	1254	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:53,913] [INFO] GTDB search result was written to GCF_004331735.1_ASM433173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:53,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:53,917] [INFO] DFAST_QC result json was written to GCF_004331735.1_ASM433173v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:53,917] [INFO] DFAST_QC completed!
[2024-01-24 15:28:53,917] [INFO] Total running time: 0h1m60s