[2024-01-25 18:02:35,485] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:35,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:35,486] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc599b35-44a6-4bac-9dec-b0a61103da93/dqc_reference
[2024-01-25 18:02:36,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:36,640] [INFO] Task started: Prodigal
[2024-01-25 18:02:36,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg8634f996-edbf-4143-9458-8aaf6dc8bf5b/GCF_000258495.1_PB92_1.0_genomic.fna.gz | prodigal -d GCF_000258495.1_PB92_1.0_genomic.fna/cds.fna -a GCF_000258495.1_PB92_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:51,901] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:51,901] [INFO] Task started: HMMsearch
[2024-01-25 18:02:51,901] [INFO] Running command: hmmsearch --tblout GCF_000258495.1_PB92_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc599b35-44a6-4bac-9dec-b0a61103da93/dqc_reference/reference_markers.hmm GCF_000258495.1_PB92_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:52,173] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:52,174] [INFO] Found 6/6 markers.
[2024-01-25 18:02:52,215] [INFO] Query marker FASTA was written to GCF_000258495.1_PB92_1.0_genomic.fna/markers.fasta
[2024-01-25 18:02:52,215] [INFO] Task started: Blastn
[2024-01-25 18:02:52,215] [INFO] Running command: blastn -query GCF_000258495.1_PB92_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc599b35-44a6-4bac-9dec-b0a61103da93/dqc_reference/reference_markers.fasta -out GCF_000258495.1_PB92_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:52,824] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:52,827] [INFO] Selected 19 target genomes.
[2024-01-25 18:02:52,827] [INFO] Target genome list was writen to GCF_000258495.1_PB92_1.0_genomic.fna/target_genomes.txt
[2024-01-25 18:02:52,844] [INFO] Task started: fastANI
[2024-01-25 18:02:52,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg8634f996-edbf-4143-9458-8aaf6dc8bf5b/GCF_000258495.1_PB92_1.0_genomic.fna.gz --refList GCF_000258495.1_PB92_1.0_genomic.fna/target_genomes.txt --output GCF_000258495.1_PB92_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:12,509] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:12,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc599b35-44a6-4bac-9dec-b0a61103da93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:12,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc599b35-44a6-4bac-9dec-b0a61103da93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:12,520] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:12,520] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:12,520] [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 agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	100.0	1515	1533	95	conclusive
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	80.8893	692	1533	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	80.7572	752	1533	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.4871	601	1533	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	80.3565	656	1533	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	80.3517	642	1533	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	80.3231	682	1533	95	below_threshold
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	80.3156	645	1533	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	80.2992	615	1533	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	80.2919	571	1533	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	80.2808	614	1533	95	below_threshold
Pedobacter petrophilus	strain=LMG 29686	GCA_009674725.1	1908241	1908241	type	True	80.2672	609	1533	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	80.2665	650	1533	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	80.1375	592	1533	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	80.1159	591	1533	95	below_threshold
Pedobacter endophyticus	strain=JBR3-12	GCA_015679185.1	2789740	2789740	type	True	79.778	545	1533	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.3639	69	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:12,521] [INFO] DFAST Taxonomy check result was written to GCF_000258495.1_PB92_1.0_genomic.fna/tc_result.tsv
[2024-01-25 18:03:12,524] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:12,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:12,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc599b35-44a6-4bac-9dec-b0a61103da93/dqc_reference/checkm_data
[2024-01-25 18:03:12,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:12,576] [INFO] Task started: CheckM
[2024-01-25 18:03:12,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000258495.1_PB92_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000258495.1_PB92_1.0_genomic.fna/checkm_input GCF_000258495.1_PB92_1.0_genomic.fna/checkm_result
[2024-01-25 18:03:57,698] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:57,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:57,719] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:57,719] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:57,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000258495.1_PB92_1.0_genomic.fna/markers.fasta)
[2024-01-25 18:03:57,720] [INFO] Task started: Blastn
[2024-01-25 18:03:57,720] [INFO] Running command: blastn -query GCF_000258495.1_PB92_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc599b35-44a6-4bac-9dec-b0a61103da93/dqc_reference/reference_markers_gtdb.fasta -out GCF_000258495.1_PB92_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:58,713] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:58,719] [INFO] Selected 17 target genomes.
[2024-01-25 18:03:58,719] [INFO] Target genome list was writen to GCF_000258495.1_PB92_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:58,730] [INFO] Task started: fastANI
[2024-01-25 18:03:58,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg8634f996-edbf-4143-9458-8aaf6dc8bf5b/GCF_000258495.1_PB92_1.0_genomic.fna.gz --refList GCF_000258495.1_PB92_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000258495.1_PB92_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:16,479] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:16,489] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:16,489] [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_000258495.1	s__Pedobacter agri	100.0	1515	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	conclusive
GCA_004210715.1	s__Pedobacter sp004210715	83.3889	687	1533	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	81.379	798	1533	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	80.8794	692	1533	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	80.7533	752	1533	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	80.3938	622	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688475.1	s__Pedobacter sp003688475	80.3866	616	1533	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	80.3515	657	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340665.1	s__Pedobacter psychrotolerans	80.3183	644	1533	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	80.3157	639	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_007994015.1	s__Pedobacter terrae_A	80.2937	617	1533	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	80.2579	610	1533	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	80.2521	638	1533	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	80.2247	649	1533	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	80.1217	589	1533	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	80.0949	540	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027745.1	s__Pedobacter sp001027745	80.0452	536	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:16,491] [INFO] GTDB search result was written to GCF_000258495.1_PB92_1.0_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:16,491] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:16,494] [INFO] DFAST_QC result json was written to GCF_000258495.1_PB92_1.0_genomic.fna/dqc_result.json
[2024-01-25 18:04:16,494] [INFO] DFAST_QC completed!
[2024-01-25 18:04:16,494] [INFO] Total running time: 0h1m41s