[2024-01-24 11:19:55,092] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg3493d942-36de-419e-8166-232a49a46f2f/dqc_reference
[2024-01-24 11:19:56,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,491] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgb481cce7-6b9d-4b99-be96-84fb865cb9cc/GCF_030409415.1_ASM3040941v1_genomic.fna.gz | prodigal -d GCF_030409415.1_ASM3040941v1_genomic.fna/cds.fna -a GCF_030409415.1_ASM3040941v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:12,636] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:12,636] [INFO] Task started: HMMsearch
[2024-01-24 11:20:12,636] [INFO] Running command: hmmsearch --tblout GCF_030409415.1_ASM3040941v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3493d942-36de-419e-8166-232a49a46f2f/dqc_reference/reference_markers.hmm GCF_030409415.1_ASM3040941v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:12,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:12,937] [INFO] Found 6/6 markers.
[2024-01-24 11:20:12,977] [INFO] Query marker FASTA was written to GCF_030409415.1_ASM3040941v1_genomic.fna/markers.fasta
[2024-01-24 11:20:12,977] [INFO] Task started: Blastn
[2024-01-24 11:20:12,977] [INFO] Running command: blastn -query GCF_030409415.1_ASM3040941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3493d942-36de-419e-8166-232a49a46f2f/dqc_reference/reference_markers.fasta -out GCF_030409415.1_ASM3040941v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:13,601] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:13,605] [INFO] Selected 18 target genomes.
[2024-01-24 11:20:13,605] [INFO] Target genome list was writen to GCF_030409415.1_ASM3040941v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:13,612] [INFO] Task started: fastANI
[2024-01-24 11:20:13,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgb481cce7-6b9d-4b99-be96-84fb865cb9cc/GCF_030409415.1_ASM3040941v1_genomic.fna.gz --refList GCF_030409415.1_ASM3040941v1_genomic.fna/target_genomes.txt --output GCF_030409415.1_ASM3040941v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:31,560] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:31,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3493d942-36de-419e-8166-232a49a46f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:31,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3493d942-36de-419e-8166-232a49a46f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:31,632] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:31,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:31,632] [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 frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	80.2956	666	1526	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	80.2733	628	1526	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	79.9591	686	1526	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	79.9581	623	1526	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	79.9139	619	1526	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	79.9117	628	1526	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	79.89	587	1526	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	79.8189	615	1526	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	79.8104	646	1526	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	79.8054	606	1526	95	below_threshold
Pedobacter petrophilus	strain=LMG 29686	GCA_009674725.1	1908241	1908241	type	True	79.7627	577	1526	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	79.7393	614	1526	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.6974	605	1526	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	79.4793	599	1526	95	below_threshold
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	79.4445	581	1526	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	78.9691	606	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:31,634] [INFO] DFAST Taxonomy check result was written to GCF_030409415.1_ASM3040941v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:31,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:31,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:31,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3493d942-36de-419e-8166-232a49a46f2f/dqc_reference/checkm_data
[2024-01-24 11:20:31,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:31,685] [INFO] Task started: CheckM
[2024-01-24 11:20:31,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409415.1_ASM3040941v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409415.1_ASM3040941v1_genomic.fna/checkm_input GCF_030409415.1_ASM3040941v1_genomic.fna/checkm_result
[2024-01-24 11:21:19,660] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:19,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:19,684] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:19,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:19,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409415.1_ASM3040941v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:19,686] [INFO] Task started: Blastn
[2024-01-24 11:21:19,686] [INFO] Running command: blastn -query GCF_030409415.1_ASM3040941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3493d942-36de-419e-8166-232a49a46f2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409415.1_ASM3040941v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:20,646] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:20,650] [INFO] Selected 21 target genomes.
[2024-01-24 11:21:20,650] [INFO] Target genome list was writen to GCF_030409415.1_ASM3040941v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:20,664] [INFO] Task started: fastANI
[2024-01-24 11:21:20,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgb481cce7-6b9d-4b99-be96-84fb865cb9cc/GCF_030409415.1_ASM3040941v1_genomic.fna.gz --refList GCF_030409415.1_ASM3040941v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409415.1_ASM3040941v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:41,705] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:41,735] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:21:41,736] [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_004331675.1	s__Pedobacter sp004331675	80.3044	665	1526	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	80.2568	629	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_001422545.1	s__Pedobacter sp001422545	80.0691	615	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173575.1	s__Pedobacter paludis	80.0133	657	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306625.1	s__Pedobacter sp014306625	79.9727	685	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310665.1	s__Pedobacter kyonggii	79.951	623	1526	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	79.9139	619	1526	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	79.883	631	1526	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	79.8779	626	1526	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	79.875	589	1526	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	79.8562	614	1526	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	79.8295	588	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_004331735.1	s__Pedobacter sp004331735	79.8106	646	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335085.1	s__Pedobacter nototheniae	79.8017	617	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.28	98.28	0.90	0.90	2	-
GCF_000708265.2	s__Pedobacter sp000708265	79.7333	602	1526	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	79.7178	614	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_003688475.1	s__Pedobacter sp003688475	79.6772	574	1526	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	79.6483	610	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCA_004210715.1	s__Pedobacter sp004210715	79.5426	453	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315595.1	s__Pedobacter miscanthi	79.4863	599	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938645.2	s__Pedobacter sp005938645	79.4767	628	1526	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 11:21:41,738] [INFO] GTDB search result was written to GCF_030409415.1_ASM3040941v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:41,739] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:41,743] [INFO] DFAST_QC result json was written to GCF_030409415.1_ASM3040941v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:41,743] [INFO] DFAST_QC completed!
[2024-01-24 11:21:41,743] [INFO] Total running time: 0h1m47s