[2024-01-24 11:09:50,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,797] [INFO] DQC Reference Directory: /var/lib/cwl/stgca894a9c-9ea1-42bc-ba50-80b733182cdd/dqc_reference
[2024-01-24 11:09:53,307] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,308] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,308] [INFO] Running command: gunzip -c /var/lib/cwl/stge1883baa-c8cc-4f93-9cd6-20800548081a/GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/cds.fna -a GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:08,125] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:08,125] [INFO] Task started: HMMsearch
[2024-01-24 11:10:08,126] [INFO] Running command: hmmsearch --tblout GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca894a9c-9ea1-42bc-ba50-80b733182cdd/dqc_reference/reference_markers.hmm GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:08,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:08,394] [INFO] Found 6/6 markers.
[2024-01-24 11:10:08,433] [INFO] Query marker FASTA was written to GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:10:08,434] [INFO] Task started: Blastn
[2024-01-24 11:10:08,434] [INFO] Running command: blastn -query GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgca894a9c-9ea1-42bc-ba50-80b733182cdd/dqc_reference/reference_markers.fasta -out GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:09,100] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:09,104] [INFO] Selected 21 target genomes.
[2024-01-24 11:10:09,104] [INFO] Target genome list was writen to GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:10:09,119] [INFO] Task started: fastANI
[2024-01-24 11:10:09,119] [INFO] Running command: fastANI --query /var/lib/cwl/stge1883baa-c8cc-4f93-9cd6-20800548081a/GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna.gz --refList GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:29,041] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:29,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca894a9c-9ea1-42bc-ba50-80b733182cdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:29,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca894a9c-9ea1-42bc-ba50-80b733182cdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:29,058] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:10:29,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:29,058] [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
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	100.0	1374	1374	95	conclusive
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	83.6081	913	1374	95	below_threshold
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	83.3965	937	1374	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	83.3171	966	1374	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	83.0841	976	1374	95	below_threshold
Chryseobacterium polytrichastri	strain=DSM 26899	GCA_900142445.1	1302687	1302687	type	True	82.0052	838	1374	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	81.7926	722	1374	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	81.5877	778	1374	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	81.2545	771	1374	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	81.252	780	1374	95	below_threshold
Chryseobacterium populi	strain=CF314	GCA_000282115.1	1144316	1144316	type	True	81.0383	795	1374	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	81.0281	752	1374	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	81.0206	741	1374	95	below_threshold
Chryseobacterium carnipullorum	strain=DSM 25581	GCA_900142785.1	1124835	1124835	type	True	80.7378	732	1374	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	80.6637	787	1374	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	80.5355	714	1374	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.4738	704	1374	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	80.2201	693	1374	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	80.2171	670	1374	95	below_threshold
Chryseobacterium indologenes	strain=NBRC 14944	GCA_000520835.1	253	253	type	True	80.1215	659	1374	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.8474	541	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:29,060] [INFO] DFAST Taxonomy check result was written to GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:10:29,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:29,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:29,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca894a9c-9ea1-42bc-ba50-80b733182cdd/dqc_reference/checkm_data
[2024-01-24 11:10:29,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:29,101] [INFO] Task started: CheckM
[2024-01-24 11:10:29,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/checkm_input GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:11:14,949] [INFO] Task succeeded: CheckM
[2024-01-24 11:11:14,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:11:14,969] [INFO] ===== Completeness check finished =====
[2024-01-24 11:11:14,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:11:14,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:11:14,970] [INFO] Task started: Blastn
[2024-01-24 11:11:14,970] [INFO] Running command: blastn -query GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgca894a9c-9ea1-42bc-ba50-80b733182cdd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:11:15,873] [INFO] Task succeeded: Blastn
[2024-01-24 11:11:15,877] [INFO] Selected 18 target genomes.
[2024-01-24 11:11:15,877] [INFO] Target genome list was writen to GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:11:15,892] [INFO] Task started: fastANI
[2024-01-24 11:11:15,892] [INFO] Running command: fastANI --query /var/lib/cwl/stge1883baa-c8cc-4f93-9cd6-20800548081a/GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna.gz --refList GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:11:34,178] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:34,206] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:11:34,206] [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_900100115.1	s__Chryseobacterium soldanellicola	100.0	1374	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000799195.1	s__Chryseobacterium sp000799195	84.1589	958	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114875.1	s__Chryseobacterium limigenitum	83.6121	912	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815655.1	s__Chryseobacterium sp003815655	83.5954	972	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648155.1	s__Chryseobacterium glaciei	83.3966	938	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	83.097	974	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456155.1	s__Chryseobacterium sp001456155	82.8258	916	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_001425355.1	s__Chryseobacterium sp001425355	82.2965	881	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045455.1	s__Chryseobacterium sp001045455	82.2511	815	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001297705.1	s__Chryseobacterium sp001297705	81.9565	851	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	81.8035	779	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813825.1	s__Chryseobacterium taiwanense	81.7315	776	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282115.1	s__Chryseobacterium populi	81.0383	795	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900142785.1	s__Chryseobacterium carnipullorum	80.7237	734	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.36	98.32	0.90	0.88	5	-
GCF_000799515.1	s__Chryseobacterium sp000799515	80.6946	697	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	80.5345	730	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754245.1	s__Chryseobacterium sp002754245	80.5337	735	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128945.1	s__Chryseobacterium sp900128945	80.504	734	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:11:34,208] [INFO] GTDB search result was written to GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:11:34,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:11:34,212] [INFO] DFAST_QC result json was written to GCF_900100115.1_IMG-taxon_2684622906_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:11:34,212] [INFO] DFAST_QC completed!
[2024-01-24 11:11:34,212] [INFO] Total running time: 0h1m43s