[2024-01-24 11:12:48,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:48,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:48,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg87bf47ea-cc35-4896-b76b-205f2b9e2eb8/dqc_reference
[2024-01-24 11:12:49,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:49,952] [INFO] Task started: Prodigal
[2024-01-24 11:12:49,953] [INFO] Running command: gunzip -c /var/lib/cwl/stgbac7b016-be94-496e-b770-303fb78f245c/GCF_007991455.1_ASM799145v1_genomic.fna.gz | prodigal -d GCF_007991455.1_ASM799145v1_genomic.fna/cds.fna -a GCF_007991455.1_ASM799145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:08,057] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:08,058] [INFO] Task started: HMMsearch
[2024-01-24 11:13:08,058] [INFO] Running command: hmmsearch --tblout GCF_007991455.1_ASM799145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87bf47ea-cc35-4896-b76b-205f2b9e2eb8/dqc_reference/reference_markers.hmm GCF_007991455.1_ASM799145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:08,326] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:08,328] [INFO] Found 6/6 markers.
[2024-01-24 11:13:08,368] [INFO] Query marker FASTA was written to GCF_007991455.1_ASM799145v1_genomic.fna/markers.fasta
[2024-01-24 11:13:08,368] [INFO] Task started: Blastn
[2024-01-24 11:13:08,368] [INFO] Running command: blastn -query GCF_007991455.1_ASM799145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87bf47ea-cc35-4896-b76b-205f2b9e2eb8/dqc_reference/reference_markers.fasta -out GCF_007991455.1_ASM799145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:08,983] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:08,988] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:08,989] [INFO] Target genome list was writen to GCF_007991455.1_ASM799145v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:09,018] [INFO] Task started: fastANI
[2024-01-24 11:13:09,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac7b016-be94-496e-b770-303fb78f245c/GCF_007991455.1_ASM799145v1_genomic.fna.gz --refList GCF_007991455.1_ASM799145v1_genomic.fna/target_genomes.txt --output GCF_007991455.1_ASM799145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:23,405] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:23,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87bf47ea-cc35-4896-b76b-205f2b9e2eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:23,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87bf47ea-cc35-4896-b76b-205f2b9e2eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:23,420] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:23,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:23,420] [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 hagamense	strain=NBRC 105253	GCA_007991455.1	395935	395935	type	True	100.0	1504	1509	95	conclusive
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	80.4223	785	1509	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	80.3675	767	1509	95	below_threshold
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	79.8829	677	1509	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	79.8501	717	1509	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	79.8144	694	1509	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	79.8037	615	1509	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	79.7797	649	1509	95	below_threshold
Chryseobacterium takakiae	strain=DSM 26898	GCA_900129385.1	1302685	1302685	type	True	79.7196	688	1509	95	below_threshold
Chryseobacterium camelliae	strain=Dolsongi-HT1	GCA_002770595.1	1265445	1265445	type	True	79.5605	627	1509	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	78.9949	575	1509	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	78.9325	542	1509	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_002943655.1	297244	297244	type	True	78.9212	520	1509	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	78.9133	516	1509	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	78.218	404	1509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,422] [INFO] DFAST Taxonomy check result was written to GCF_007991455.1_ASM799145v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:23,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:23,423] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:23,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87bf47ea-cc35-4896-b76b-205f2b9e2eb8/dqc_reference/checkm_data
[2024-01-24 11:13:23,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:23,473] [INFO] Task started: CheckM
[2024-01-24 11:13:23,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991455.1_ASM799145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991455.1_ASM799145v1_genomic.fna/checkm_input GCF_007991455.1_ASM799145v1_genomic.fna/checkm_result
[2024-01-24 11:14:17,097] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:17,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:17,118] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:17,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:17,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991455.1_ASM799145v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:17,119] [INFO] Task started: Blastn
[2024-01-24 11:14:17,119] [INFO] Running command: blastn -query GCF_007991455.1_ASM799145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87bf47ea-cc35-4896-b76b-205f2b9e2eb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991455.1_ASM799145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:17,987] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:17,991] [INFO] Selected 17 target genomes.
[2024-01-24 11:14:17,991] [INFO] Target genome list was writen to GCF_007991455.1_ASM799145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:18,008] [INFO] Task started: fastANI
[2024-01-24 11:14:18,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac7b016-be94-496e-b770-303fb78f245c/GCF_007991455.1_ASM799145v1_genomic.fna.gz --refList GCF_007991455.1_ASM799145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991455.1_ASM799145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:33,707] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:33,733] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:33,733] [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_007991455.1	s__Chryseobacterium hagamense	100.0	1504	1509	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_008329705.1	s__Chryseobacterium sp008329705	86.5016	1179	1509	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	80.4146	786	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_002177115.1	s__Chryseobacterium mucoviscidosis	80.3749	766	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCF_018603435.1	s__Chryseobacterium sp013153155	80.2259	769	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.28	96.28	0.93	0.93	2	-
GCF_001421435.1	s__Chryseobacterium sp001421435	79.9207	729	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708615.2	s__Chryseobacterium hispalense	79.8677	679	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.96	98.96	0.90	0.90	2	-
GCF_000430845.1	s__Chryseobacterium gregarium	79.8376	684	1509	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	79.8356	719	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927265.1	s__Chryseobacterium cheonjiense	79.8216	693	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430825.1	s__Chryseobacterium daeguense	79.8003	617	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434285.1	s__Chryseobacterium sp002434285	79.7789	592	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333355.1	s__Chryseobacterium sp000333355	79.7634	539	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129385.1	s__Chryseobacterium takakiae	79.7348	686	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002770595.1	s__Chryseobacterium camelliae	79.5686	626	1509	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	79.3547	607	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_900115055.1	s__Chryseobacterium oleae	78.9249	542	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:33,735] [INFO] GTDB search result was written to GCF_007991455.1_ASM799145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:33,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:33,739] [INFO] DFAST_QC result json was written to GCF_007991455.1_ASM799145v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:33,740] [INFO] DFAST_QC completed!
[2024-01-24 11:14:33,740] [INFO] Total running time: 0h1m45s