[2024-01-24 13:31:44,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cae485b-2255-4224-b310-1e797edf9737/dqc_reference
[2024-01-24 13:31:45,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,605] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg69e28148-0cef-479a-a234-52daff9188d3/GCF_009674725.1_ASM967472v1_genomic.fna.gz | prodigal -d GCF_009674725.1_ASM967472v1_genomic.fna/cds.fna -a GCF_009674725.1_ASM967472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:05,369] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:05,370] [INFO] Task started: HMMsearch
[2024-01-24 13:32:05,370] [INFO] Running command: hmmsearch --tblout GCF_009674725.1_ASM967472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cae485b-2255-4224-b310-1e797edf9737/dqc_reference/reference_markers.hmm GCF_009674725.1_ASM967472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:05,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:05,727] [INFO] Found 6/6 markers.
[2024-01-24 13:32:05,782] [INFO] Query marker FASTA was written to GCF_009674725.1_ASM967472v1_genomic.fna/markers.fasta
[2024-01-24 13:32:05,783] [INFO] Task started: Blastn
[2024-01-24 13:32:05,783] [INFO] Running command: blastn -query GCF_009674725.1_ASM967472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cae485b-2255-4224-b310-1e797edf9737/dqc_reference/reference_markers.fasta -out GCF_009674725.1_ASM967472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,461] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,464] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:06,464] [INFO] Target genome list was writen to GCF_009674725.1_ASM967472v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:06,478] [INFO] Task started: fastANI
[2024-01-24 13:32:06,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e28148-0cef-479a-a234-52daff9188d3/GCF_009674725.1_ASM967472v1_genomic.fna.gz --refList GCF_009674725.1_ASM967472v1_genomic.fna/target_genomes.txt --output GCF_009674725.1_ASM967472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:24,692] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:24,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cae485b-2255-4224-b310-1e797edf9737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:24,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cae485b-2255-4224-b310-1e797edf9737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:24,707] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:24,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:24,707] [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 petrophilus	strain=LMG 29686	GCA_009674725.1	1908241	1908241	type	True	100.0	1760	1765	95	conclusive
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	81.5954	995	1765	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	81.5691	986	1765	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.2697	641	1765	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	80.2678	625	1765	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	80.2423	681	1765	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	80.1825	697	1765	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	80.0542	634	1765	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	79.9578	672	1765	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	79.9487	722	1765	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.7812	641	1765	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	79.7558	671	1765	95	below_threshold
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	79.4486	536	1765	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	79.3218	545	1765	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	77.052	53	1765	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.2474	65	1765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:24,710] [INFO] DFAST Taxonomy check result was written to GCF_009674725.1_ASM967472v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:24,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:24,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:24,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cae485b-2255-4224-b310-1e797edf9737/dqc_reference/checkm_data
[2024-01-24 13:32:24,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:24,776] [INFO] Task started: CheckM
[2024-01-24 13:32:24,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674725.1_ASM967472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674725.1_ASM967472v1_genomic.fna/checkm_input GCF_009674725.1_ASM967472v1_genomic.fna/checkm_result
[2024-01-24 13:33:22,560] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:22,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:22,588] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:22,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:22,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674725.1_ASM967472v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:22,589] [INFO] Task started: Blastn
[2024-01-24 13:33:22,589] [INFO] Running command: blastn -query GCF_009674725.1_ASM967472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cae485b-2255-4224-b310-1e797edf9737/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674725.1_ASM967472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:23,496] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:23,503] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:23,503] [INFO] Target genome list was writen to GCF_009674725.1_ASM967472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:23,514] [INFO] Task started: fastANI
[2024-01-24 13:33:23,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e28148-0cef-479a-a234-52daff9188d3/GCF_009674725.1_ASM967472v1_genomic.fna.gz --refList GCF_009674725.1_ASM967472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674725.1_ASM967472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:39,542] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:39,557] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:39,557] [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_009674725.1	s__Pedobacter petrophilus	100.0	1760	1765	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_004340665.1	s__Pedobacter psychrotolerans	81.5841	997	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000708265.2	s__Pedobacter sp000708265	81.282	990	1765	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	81.2137	944	1765	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	80.2599	627	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_003664035.1	s__Pedobacter alluvionis	80.2296	684	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002151545.1	s__Pedobacter sp002151545	80.055	673	1765	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	80.0487	667	1765	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	80.0259	722	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_018613605.1	s__Pedobacter sp018613605	79.998	674	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_004331675.1	s__Pedobacter sp004331675	79.95	673	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633455.1	s__Pedobacter jeongneungensis	79.8989	710	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725795.1	s__Pedobacter jejuensis	79.6579	624	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210715.1	s__Pedobacter sp004210715	79.528	452	1765	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 13:33:39,563] [INFO] GTDB search result was written to GCF_009674725.1_ASM967472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:39,565] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:39,579] [INFO] DFAST_QC result json was written to GCF_009674725.1_ASM967472v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:39,579] [INFO] DFAST_QC completed!
[2024-01-24 13:33:39,579] [INFO] Total running time: 0h1m55s