[2024-01-25 18:37:20,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:20,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:20,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg89fd331a-129b-40ef-91bd-c5ea4fbc4d5b/dqc_reference
[2024-01-25 18:37:21,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:21,699] [INFO] Task started: Prodigal
[2024-01-25 18:37:21,700] [INFO] Running command: gunzip -c /var/lib/cwl/stgddaf6ddf-4e72-4c54-a8fd-ae7983b0997d/GCF_025628985.1_ASM2562898v1_genomic.fna.gz | prodigal -d GCF_025628985.1_ASM2562898v1_genomic.fna/cds.fna -a GCF_025628985.1_ASM2562898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:34,373] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:34,373] [INFO] Task started: HMMsearch
[2024-01-25 18:37:34,373] [INFO] Running command: hmmsearch --tblout GCF_025628985.1_ASM2562898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89fd331a-129b-40ef-91bd-c5ea4fbc4d5b/dqc_reference/reference_markers.hmm GCF_025628985.1_ASM2562898v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:34,610] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:34,611] [INFO] Found 6/6 markers.
[2024-01-25 18:37:34,652] [INFO] Query marker FASTA was written to GCF_025628985.1_ASM2562898v1_genomic.fna/markers.fasta
[2024-01-25 18:37:34,653] [INFO] Task started: Blastn
[2024-01-25 18:37:34,653] [INFO] Running command: blastn -query GCF_025628985.1_ASM2562898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89fd331a-129b-40ef-91bd-c5ea4fbc4d5b/dqc_reference/reference_markers.fasta -out GCF_025628985.1_ASM2562898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:35,280] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:35,286] [INFO] Selected 19 target genomes.
[2024-01-25 18:37:35,287] [INFO] Target genome list was writen to GCF_025628985.1_ASM2562898v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:35,347] [INFO] Task started: fastANI
[2024-01-25 18:37:35,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgddaf6ddf-4e72-4c54-a8fd-ae7983b0997d/GCF_025628985.1_ASM2562898v1_genomic.fna.gz --refList GCF_025628985.1_ASM2562898v1_genomic.fna/target_genomes.txt --output GCF_025628985.1_ASM2562898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:37:50,950] [INFO] Task succeeded: fastANI
[2024-01-25 18:37:50,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89fd331a-129b-40ef-91bd-c5ea4fbc4d5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:37:50,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89fd331a-129b-40ef-91bd-c5ea4fbc4d5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:37:50,962] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:37:50,962] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:37:50,962] [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	84.0476	871	1368	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	84.0436	908	1368	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	82.245	846	1368	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	82.2418	842	1368	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	82.1895	817	1368	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	82.1401	871	1368	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	82.0684	845	1368	95	below_threshold
Chryseobacterium caseinilyticum	strain=GCR10	GCA_014837145.1	2771428	2771428	type	True	82.0353	727	1368	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	81.7727	815	1368	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	81.5724	816	1368	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	81.2101	626	1368	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_002943675.1	551459	551459	type	True	81.2056	613	1368	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.972	789	1368	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.1949	651	1368	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.0228	686	1368	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	79.9244	675	1368	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	79.7487	669	1368	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.6625	405	1368	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.2505	211	1368	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:37:50,964] [INFO] DFAST Taxonomy check result was written to GCF_025628985.1_ASM2562898v1_genomic.fna/tc_result.tsv
[2024-01-25 18:37:50,964] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:37:50,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:37:50,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89fd331a-129b-40ef-91bd-c5ea4fbc4d5b/dqc_reference/checkm_data
[2024-01-25 18:37:50,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:37:51,011] [INFO] Task started: CheckM
[2024-01-25 18:37:51,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025628985.1_ASM2562898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025628985.1_ASM2562898v1_genomic.fna/checkm_input GCF_025628985.1_ASM2562898v1_genomic.fna/checkm_result
[2024-01-25 18:38:31,177] [INFO] Task succeeded: CheckM
[2024-01-25 18:38:31,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:38:31,200] [INFO] ===== Completeness check finished =====
[2024-01-25 18:38:31,201] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:38:31,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025628985.1_ASM2562898v1_genomic.fna/markers.fasta)
[2024-01-25 18:38:31,202] [INFO] Task started: Blastn
[2024-01-25 18:38:31,202] [INFO] Running command: blastn -query GCF_025628985.1_ASM2562898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89fd331a-129b-40ef-91bd-c5ea4fbc4d5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025628985.1_ASM2562898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:32,116] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:32,119] [INFO] Selected 9 target genomes.
[2024-01-25 18:38:32,119] [INFO] Target genome list was writen to GCF_025628985.1_ASM2562898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:38:32,124] [INFO] Task started: fastANI
[2024-01-25 18:38:32,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgddaf6ddf-4e72-4c54-a8fd-ae7983b0997d/GCF_025628985.1_ASM2562898v1_genomic.fna.gz --refList GCF_025628985.1_ASM2562898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025628985.1_ASM2562898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:38:40,749] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:40,755] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:38:40,756] [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_000799255.1	s__Chryseobacterium sp000799255	85.3905	923	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.94	98.94	0.94	0.94	2	-
GCF_003669035.1	s__Chryseobacterium sp003669035	85.1324	969	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728305.1	s__Chryseobacterium sp902728305	84.1587	843	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012952015.1	s__Chryseobacterium aquaticum_A	84.0706	886	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.4843	100.00	100.00	1.00	1.00	2	-
GCF_001420285.1	s__Chryseobacterium aquaticum	84.064	869	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	96.87	96.87	0.89	0.89	2	-
GCF_001507325.1	s__Chryseobacterium greenlandense	84.052	907	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
GCF_001424105.1	s__Chryseobacterium sp001424105	82.2556	705	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815915.1	s__Chryseobacterium indoltheticum	82.2515	845	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_001424145.1	s__Chryseobacterium sp001424145	80.848	684	1368	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 18:38:40,769] [INFO] GTDB search result was written to GCF_025628985.1_ASM2562898v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:38:40,769] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:38:40,772] [INFO] DFAST_QC result json was written to GCF_025628985.1_ASM2562898v1_genomic.fna/dqc_result.json
[2024-01-25 18:38:40,772] [INFO] DFAST_QC completed!
[2024-01-25 18:38:40,772] [INFO] Total running time: 0h1m20s