[2024-01-25 20:07:05,480] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:05,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:05,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8538cbd-3d9d-46f2-b279-68973b3a3a3f/dqc_reference
[2024-01-25 20:07:06,608] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:06,609] [INFO] Task started: Prodigal
[2024-01-25 20:07:06,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg4574c301-eb32-411b-9762-297dfecb175c/GCF_016735585.2_ASM1673558v2_genomic.fna.gz | prodigal -d GCF_016735585.2_ASM1673558v2_genomic.fna/cds.fna -a GCF_016735585.2_ASM1673558v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:19,827] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:19,827] [INFO] Task started: HMMsearch
[2024-01-25 20:07:19,828] [INFO] Running command: hmmsearch --tblout GCF_016735585.2_ASM1673558v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8538cbd-3d9d-46f2-b279-68973b3a3a3f/dqc_reference/reference_markers.hmm GCF_016735585.2_ASM1673558v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:20,082] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:20,083] [INFO] Found 6/6 markers.
[2024-01-25 20:07:20,121] [INFO] Query marker FASTA was written to GCF_016735585.2_ASM1673558v2_genomic.fna/markers.fasta
[2024-01-25 20:07:20,122] [INFO] Task started: Blastn
[2024-01-25 20:07:20,122] [INFO] Running command: blastn -query GCF_016735585.2_ASM1673558v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8538cbd-3d9d-46f2-b279-68973b3a3a3f/dqc_reference/reference_markers.fasta -out GCF_016735585.2_ASM1673558v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:20,759] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:20,761] [INFO] Selected 14 target genomes.
[2024-01-25 20:07:20,762] [INFO] Target genome list was writen to GCF_016735585.2_ASM1673558v2_genomic.fna/target_genomes.txt
[2024-01-25 20:07:20,767] [INFO] Task started: fastANI
[2024-01-25 20:07:20,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg4574c301-eb32-411b-9762-297dfecb175c/GCF_016735585.2_ASM1673558v2_genomic.fna.gz --refList GCF_016735585.2_ASM1673558v2_genomic.fna/target_genomes.txt --output GCF_016735585.2_ASM1673558v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:34,330] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:34,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8538cbd-3d9d-46f2-b279-68973b3a3a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:34,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8538cbd-3d9d-46f2-b279-68973b3a3a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:34,339] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:34,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:34,340] [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 tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	100.0	1472	1473	95	conclusive
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	86.5269	1096	1473	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	86.3703	959	1473	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	82.3819	890	1473	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	82.2931	912	1473	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	82.2882	827	1473	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	81.5515	810	1473	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	80.8957	744	1473	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	80.8623	769	1473	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	80.8373	733	1473	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	80.5652	715	1473	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.454	726	1473	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	80.2758	708	1473	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.4988	498	1473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:34,341] [INFO] DFAST Taxonomy check result was written to GCF_016735585.2_ASM1673558v2_genomic.fna/tc_result.tsv
[2024-01-25 20:07:34,341] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:34,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:34,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8538cbd-3d9d-46f2-b279-68973b3a3a3f/dqc_reference/checkm_data
[2024-01-25 20:07:34,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:34,389] [INFO] Task started: CheckM
[2024-01-25 20:07:34,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016735585.2_ASM1673558v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016735585.2_ASM1673558v2_genomic.fna/checkm_input GCF_016735585.2_ASM1673558v2_genomic.fna/checkm_result
[2024-01-25 20:08:15,473] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:15,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:15,504] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:15,504] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:15,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016735585.2_ASM1673558v2_genomic.fna/markers.fasta)
[2024-01-25 20:08:15,505] [INFO] Task started: Blastn
[2024-01-25 20:08:15,505] [INFO] Running command: blastn -query GCF_016735585.2_ASM1673558v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8538cbd-3d9d-46f2-b279-68973b3a3a3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016735585.2_ASM1673558v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:16,425] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:16,428] [INFO] Selected 15 target genomes.
[2024-01-25 20:08:16,429] [INFO] Target genome list was writen to GCF_016735585.2_ASM1673558v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:16,442] [INFO] Task started: fastANI
[2024-01-25 20:08:16,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg4574c301-eb32-411b-9762-297dfecb175c/GCF_016735585.2_ASM1673558v2_genomic.fna.gz --refList GCF_016735585.2_ASM1673558v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016735585.2_ASM1673558v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:31,293] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:31,302] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:08:31,303] [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_000813825.1	s__Chryseobacterium taiwanense	88.9585	1131	1473	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	88.4046	1146	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	86.5218	1096	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCF_000799195.1	s__Chryseobacterium sp000799195	82.4845	871	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129245.1	s__Chryseobacterium arachidis	82.3975	888	1473	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	82.2839	828	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425355.1	s__Chryseobacterium sp001425355	81.8199	832	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156825.1	s__Chryseobacterium gambrini	81.5603	809	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_000799515.1	s__Chryseobacterium sp000799515	81.1605	679	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116415.1	s__Chryseobacterium formosense	80.895	745	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.74	97.50	0.90	0.80	3	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	80.8413	772	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	80.8287	734	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799235.1	s__Chryseobacterium sp000799235	80.5816	782	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684955.1	s__Chryseobacterium contaminans	80.4015	672	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900128945.1	s__Chryseobacterium sp900128945	80.0444	725	1473	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:31,304] [INFO] GTDB search result was written to GCF_016735585.2_ASM1673558v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:31,305] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:31,308] [INFO] DFAST_QC result json was written to GCF_016735585.2_ASM1673558v2_genomic.fna/dqc_result.json
[2024-01-25 20:08:31,308] [INFO] DFAST_QC completed!
[2024-01-25 20:08:31,308] [INFO] Total running time: 0h1m26s