[2024-01-25 18:13:36,422] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:36,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:36,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f212f9f-eeea-4d72-a0ab-535dcf4c4a4e/dqc_reference
[2024-01-25 18:13:37,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:37,548] [INFO] Task started: Prodigal
[2024-01-25 18:13:37,548] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0d7c1c1-041b-429a-93db-26cdfb79a9df/GCF_025403485.1_ASM2540348v1_genomic.fna.gz | prodigal -d GCF_025403485.1_ASM2540348v1_genomic.fna/cds.fna -a GCF_025403485.1_ASM2540348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:51,880] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:51,881] [INFO] Task started: HMMsearch
[2024-01-25 18:13:51,881] [INFO] Running command: hmmsearch --tblout GCF_025403485.1_ASM2540348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f212f9f-eeea-4d72-a0ab-535dcf4c4a4e/dqc_reference/reference_markers.hmm GCF_025403485.1_ASM2540348v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:52,139] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:52,140] [INFO] Found 6/6 markers.
[2024-01-25 18:13:52,181] [INFO] Query marker FASTA was written to GCF_025403485.1_ASM2540348v1_genomic.fna/markers.fasta
[2024-01-25 18:13:52,181] [INFO] Task started: Blastn
[2024-01-25 18:13:52,181] [INFO] Running command: blastn -query GCF_025403485.1_ASM2540348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f212f9f-eeea-4d72-a0ab-535dcf4c4a4e/dqc_reference/reference_markers.fasta -out GCF_025403485.1_ASM2540348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:52,792] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:52,796] [INFO] Selected 17 target genomes.
[2024-01-25 18:13:52,796] [INFO] Target genome list was writen to GCF_025403485.1_ASM2540348v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:52,804] [INFO] Task started: fastANI
[2024-01-25 18:13:52,805] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d7c1c1-041b-429a-93db-26cdfb79a9df/GCF_025403485.1_ASM2540348v1_genomic.fna.gz --refList GCF_025403485.1_ASM2540348v1_genomic.fna/target_genomes.txt --output GCF_025403485.1_ASM2540348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:08,784] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:08,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f212f9f-eeea-4d72-a0ab-535dcf4c4a4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:08,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f212f9f-eeea-4d72-a0ab-535dcf4c4a4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:08,795] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:08,795] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:08,795] [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 paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	83.9775	1228	1683	95	below_threshold
Chryseobacterium piperi	strain=ATCC BAA-1782	GCA_002285635.2	558152	558152	type	True	82.4286	992	1683	95	below_threshold
Chryseobacterium piperi	strain=CTM	GCA_000737775.1	558152	558152	type	True	82.364	969	1683	95	below_threshold
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	80.7928	857	1683	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	80.7687	829	1683	95	below_threshold
Chryseobacterium polytrichastri	strain=DSM 26899	GCA_900142445.1	1302687	1302687	type	True	80.5556	873	1683	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	80.3035	766	1683	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.1744	770	1683	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	80.0578	723	1683	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	80.0289	719	1683	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.0274	680	1683	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	79.9627	782	1683	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	79.9475	778	1683	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	79.8781	727	1683	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.4104	624	1683	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.2861	554	1683	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.5297	187	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:08,796] [INFO] DFAST Taxonomy check result was written to GCF_025403485.1_ASM2540348v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:08,797] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:08,797] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:08,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f212f9f-eeea-4d72-a0ab-535dcf4c4a4e/dqc_reference/checkm_data
[2024-01-25 18:14:08,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:08,845] [INFO] Task started: CheckM
[2024-01-25 18:14:08,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025403485.1_ASM2540348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025403485.1_ASM2540348v1_genomic.fna/checkm_input GCF_025403485.1_ASM2540348v1_genomic.fna/checkm_result
[2024-01-25 18:14:52,077] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:52,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:52,125] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:52,126] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:52,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025403485.1_ASM2540348v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:52,126] [INFO] Task started: Blastn
[2024-01-25 18:14:52,126] [INFO] Running command: blastn -query GCF_025403485.1_ASM2540348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f212f9f-eeea-4d72-a0ab-535dcf4c4a4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025403485.1_ASM2540348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:53,018] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:53,020] [INFO] Selected 9 target genomes.
[2024-01-25 18:14:53,021] [INFO] Target genome list was writen to GCF_025403485.1_ASM2540348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:53,035] [INFO] Task started: fastANI
[2024-01-25 18:14:53,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d7c1c1-041b-429a-93db-26cdfb79a9df/GCF_025403485.1_ASM2540348v1_genomic.fna.gz --refList GCF_025403485.1_ASM2540348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025403485.1_ASM2540348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:03,177] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:03,183] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:03,184] [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_018613715.1	s__Chryseobacterium sp018613715	99.0857	1491	1683	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_016595215.1	s__Chryseobacterium sp016595215	83.9979	1224	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216065.1	s__Chryseobacterium sp002216065	83.6969	1220	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285635.2	s__Chryseobacterium piperi	82.4285	992	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013184525.1	s__Chryseobacterium sp013184525	82.366	1097	1683	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	80.8529	878	1683	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	80.7765	828	1683	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	80.6623	880	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142445.1	s__Chryseobacterium polytrichastri	80.5519	875	1683	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 18:15:03,185] [INFO] GTDB search result was written to GCF_025403485.1_ASM2540348v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:03,186] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:03,189] [INFO] DFAST_QC result json was written to GCF_025403485.1_ASM2540348v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:03,189] [INFO] DFAST_QC completed!
[2024-01-25 18:15:03,189] [INFO] Total running time: 0h1m27s