[2024-01-25 18:25:20,615] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:20,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:20,617] [INFO] DQC Reference Directory: /var/lib/cwl/stgf435a7c6-0bf1-4a7d-8b93-6f636a4e226e/dqc_reference
[2024-01-25 18:25:21,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:21,723] [INFO] Task started: Prodigal
[2024-01-25 18:25:21,724] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb67c283-779a-4cef-b25d-0c8272648342/GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna.gz | prodigal -d GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/cds.fna -a GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:32,915] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:32,916] [INFO] Task started: HMMsearch
[2024-01-25 18:25:32,916] [INFO] Running command: hmmsearch --tblout GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf435a7c6-0bf1-4a7d-8b93-6f636a4e226e/dqc_reference/reference_markers.hmm GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:33,143] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:33,144] [INFO] Found 6/6 markers.
[2024-01-25 18:25:33,174] [INFO] Query marker FASTA was written to GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/markers.fasta
[2024-01-25 18:25:33,174] [INFO] Task started: Blastn
[2024-01-25 18:25:33,174] [INFO] Running command: blastn -query GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/markers.fasta -db /var/lib/cwl/stgf435a7c6-0bf1-4a7d-8b93-6f636a4e226e/dqc_reference/reference_markers.fasta -out GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:33,772] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:33,775] [INFO] Selected 20 target genomes.
[2024-01-25 18:25:33,776] [INFO] Target genome list was writen to GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/target_genomes.txt
[2024-01-25 18:25:33,792] [INFO] Task started: fastANI
[2024-01-25 18:25:33,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb67c283-779a-4cef-b25d-0c8272648342/GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna.gz --refList GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/target_genomes.txt --output GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:50,289] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:50,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf435a7c6-0bf1-4a7d-8b93-6f636a4e226e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:50,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf435a7c6-0bf1-4a7d-8b93-6f636a4e226e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:50,301] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:25:50,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:25:50,302] [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 aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	83.3583	810	1163	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	83.1652	822	1163	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	81.8791	731	1163	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	81.865	734	1163	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	81.8127	717	1163	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	81.4312	741	1163	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	81.077	610	1163	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	80.9861	718	1163	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_002943675.1	551459	551459	type	True	80.9725	610	1163	95	below_threshold
Chryseobacterium caseinilyticum	strain=GCR10	GCA_014837145.1	2771428	2771428	type	True	80.6899	639	1163	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.6203	678	1163	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	80.3575	600	1163	95	below_threshold
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	80.3098	678	1163	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.0211	545	1163	95	below_threshold
Chryseobacterium echinoideorum	strain=CC-CZW010	GCA_007474535.1	1549648	1549648	type	True	79.9639	581	1163	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.7528	602	1163	95	below_threshold
Chryseobacterium populi	strain=CF314	GCA_000282115.1	1144316	1144316	type	True	79.0945	522	1163	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	78.9852	473	1163	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	78.9014	477	1163	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.5672	187	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:50,304] [INFO] DFAST Taxonomy check result was written to GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/tc_result.tsv
[2024-01-25 18:25:50,304] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:50,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:50,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf435a7c6-0bf1-4a7d-8b93-6f636a4e226e/dqc_reference/checkm_data
[2024-01-25 18:25:50,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:50,343] [INFO] Task started: CheckM
[2024-01-25 18:25:50,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/checkm_input GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/checkm_result
[2024-01-25 18:26:26,144] [INFO] Task succeeded: CheckM
[2024-01-25 18:26:26,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:26:26,160] [INFO] ===== Completeness check finished =====
[2024-01-25 18:26:26,160] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:26:26,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/markers.fasta)
[2024-01-25 18:26:26,161] [INFO] Task started: Blastn
[2024-01-25 18:26:26,162] [INFO] Running command: blastn -query GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/markers.fasta -db /var/lib/cwl/stgf435a7c6-0bf1-4a7d-8b93-6f636a4e226e/dqc_reference/reference_markers_gtdb.fasta -out GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:26:26,989] [INFO] Task succeeded: Blastn
[2024-01-25 18:26:26,993] [INFO] Selected 11 target genomes.
[2024-01-25 18:26:26,993] [INFO] Target genome list was writen to GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:26:27,004] [INFO] Task started: fastANI
[2024-01-25 18:26:27,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb67c283-779a-4cef-b25d-0c8272648342/GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna.gz --refList GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/target_genomes_gtdb.txt --output GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:26:36,458] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:36,467] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:26:36,467] [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_902728305.1	s__Chryseobacterium sp902728305	100.0	1156	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003669035.1	s__Chryseobacterium sp003669035	84.6907	861	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799255.1	s__Chryseobacterium sp000799255	83.4299	808	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.94	98.94	0.94	0.94	2	-
GCF_001420285.1	s__Chryseobacterium aquaticum	83.3504	811	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	96.87	96.87	0.89	0.89	2	-
GCF_012952015.1	s__Chryseobacterium aquaticum_A	83.2476	821	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.4843	100.00	100.00	1.00	1.00	2	-
GCF_001507325.1	s__Chryseobacterium greenlandense	83.1705	821	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
GCF_000745795.1	s__Chryseobacterium sp000745795	82.2256	665	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156685.1	s__Chryseobacterium piscicola	81.0387	614	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014837145.1	s__Chryseobacterium caseinilyticum	80.671	641	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424105.1	s__Chryseobacterium sp001424105	80.6171	648	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424145.1	s__Chryseobacterium sp001424145	80.5565	602	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:26:36,468] [INFO] GTDB search result was written to GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/result_gtdb.tsv
[2024-01-25 18:26:36,469] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:26:36,473] [INFO] DFAST_QC result json was written to GCF_905175375.1_Chryseobacterium_CECT9390_genomic.fna/dqc_result.json
[2024-01-25 18:26:36,473] [INFO] DFAST_QC completed!
[2024-01-25 18:26:36,473] [INFO] Total running time: 0h1m16s