[2024-01-25 18:49:35,534] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:35,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:35,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ea99032-3b33-42a8-a7a9-6dcd4d144af5/dqc_reference
[2024-01-25 18:49:36,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:36,626] [INFO] Task started: Prodigal
[2024-01-25 18:49:36,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ead5020-e6b9-4c81-8173-5dea423c6e11/GCF_015679185.1_ASM1567918v1_genomic.fna.gz | prodigal -d GCF_015679185.1_ASM1567918v1_genomic.fna/cds.fna -a GCF_015679185.1_ASM1567918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:55,904] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:55,904] [INFO] Task started: HMMsearch
[2024-01-25 18:49:55,904] [INFO] Running command: hmmsearch --tblout GCF_015679185.1_ASM1567918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ea99032-3b33-42a8-a7a9-6dcd4d144af5/dqc_reference/reference_markers.hmm GCF_015679185.1_ASM1567918v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:56,180] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:56,181] [INFO] Found 6/6 markers.
[2024-01-25 18:49:56,223] [INFO] Query marker FASTA was written to GCF_015679185.1_ASM1567918v1_genomic.fna/markers.fasta
[2024-01-25 18:49:56,223] [INFO] Task started: Blastn
[2024-01-25 18:49:56,224] [INFO] Running command: blastn -query GCF_015679185.1_ASM1567918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ea99032-3b33-42a8-a7a9-6dcd4d144af5/dqc_reference/reference_markers.fasta -out GCF_015679185.1_ASM1567918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:56,785] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:56,788] [INFO] Selected 18 target genomes.
[2024-01-25 18:49:56,788] [INFO] Target genome list was writen to GCF_015679185.1_ASM1567918v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:56,805] [INFO] Task started: fastANI
[2024-01-25 18:49:56,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ead5020-e6b9-4c81-8173-5dea423c6e11/GCF_015679185.1_ASM1567918v1_genomic.fna.gz --refList GCF_015679185.1_ASM1567918v1_genomic.fna/target_genomes.txt --output GCF_015679185.1_ASM1567918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:17,620] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:17,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ea99032-3b33-42a8-a7a9-6dcd4d144af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:17,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ea99032-3b33-42a8-a7a9-6dcd4d144af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:17,631] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:50:17,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:17,631] [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 endophyticus	strain=JBR3-12	GCA_015679185.1	2789740	2789740	type	True	100.0	1808	1808	95	conclusive
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	79.6375	549	1808	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	79.6353	631	1808	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	79.6315	648	1808	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	79.6179	601	1808	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	79.4821	639	1808	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	79.457	675	1808	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	79.358	611	1808	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	79.3522	642	1808	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	79.3216	608	1808	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.3203	640	1808	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	79.3171	537	1808	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	79.3032	630	1808	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	79.2986	608	1808	95	below_threshold
Pedobacter suwonensis	strain=DSM 18130	GCA_900111825.1	332999	332999	type	True	78.9243	584	1808	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	77.774	81	1808	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	76.7988	50	1808	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.4283	61	1808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:17,633] [INFO] DFAST Taxonomy check result was written to GCF_015679185.1_ASM1567918v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:17,634] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:17,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:17,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ea99032-3b33-42a8-a7a9-6dcd4d144af5/dqc_reference/checkm_data
[2024-01-25 18:50:17,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:17,687] [INFO] Task started: CheckM
[2024-01-25 18:50:17,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015679185.1_ASM1567918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015679185.1_ASM1567918v1_genomic.fna/checkm_input GCF_015679185.1_ASM1567918v1_genomic.fna/checkm_result
[2024-01-25 18:51:11,742] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:11,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:11,763] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:11,763] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:11,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015679185.1_ASM1567918v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:11,764] [INFO] Task started: Blastn
[2024-01-25 18:51:11,764] [INFO] Running command: blastn -query GCF_015679185.1_ASM1567918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ea99032-3b33-42a8-a7a9-6dcd4d144af5/dqc_reference/reference_markers_gtdb.fasta -out GCF_015679185.1_ASM1567918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:12,621] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:12,627] [INFO] Selected 21 target genomes.
[2024-01-25 18:51:12,627] [INFO] Target genome list was writen to GCF_015679185.1_ASM1567918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:12,685] [INFO] Task started: fastANI
[2024-01-25 18:51:12,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ead5020-e6b9-4c81-8173-5dea423c6e11/GCF_015679185.1_ASM1567918v1_genomic.fna.gz --refList GCF_015679185.1_ASM1567918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015679185.1_ASM1567918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:38,464] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:38,477] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:38,477] [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_015679185.1	s__Pedobacter sp015679185	100.0	1808	1808	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_001421515.1	s__Pedobacter sp001421515	79.6999	646	1808	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	79.6467	548	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_004331675.1	s__Pedobacter sp004331675	79.6349	648	1808	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	79.6249	639	1808	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	79.6113	603	1808	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	79.5022	613	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_003315595.1	s__Pedobacter miscanthi	79.4779	638	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422545.1	s__Pedobacter sp001422545	79.4746	597	1808	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	79.4487	621	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	79.4394	678	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054145.1	s__Pedobacter sp003054145	79.4179	630	1808	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	79.3924	644	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205835.1	s__Pedobacter sp014205835	79.3764	617	1808	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	79.3743	641	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909215.1	s__Pedobacter terrae_B	79.3013	561	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708265.2	s__Pedobacter sp000708265	79.223	532	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424305.1	s__Pedobacter sp001424305	79.1363	488	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432345.1	s__Pedobacter sp002432345	79.1263	594	1808	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	79.002	514	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111825.1	s__Pedobacter suwonensis	78.9285	585	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.36	97.36	0.90	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:38,478] [INFO] GTDB search result was written to GCF_015679185.1_ASM1567918v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:38,479] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:38,483] [INFO] DFAST_QC result json was written to GCF_015679185.1_ASM1567918v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:38,483] [INFO] DFAST_QC completed!
[2024-01-25 18:51:38,483] [INFO] Total running time: 0h2m3s