[2024-01-25 18:58:05,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:05,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:05,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg0af51296-d4a0-4983-9900-aaa4522f96f3/dqc_reference
[2024-01-25 18:58:06,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:06,943] [INFO] Task started: Prodigal
[2024-01-25 18:58:06,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg656bfae6-8a70-4301-9348-35609c9f4260/GCF_014837145.1_ASM1483714v1_genomic.fna.gz | prodigal -d GCF_014837145.1_ASM1483714v1_genomic.fna/cds.fna -a GCF_014837145.1_ASM1483714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:20,440] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:20,441] [INFO] Task started: HMMsearch
[2024-01-25 18:58:20,441] [INFO] Running command: hmmsearch --tblout GCF_014837145.1_ASM1483714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0af51296-d4a0-4983-9900-aaa4522f96f3/dqc_reference/reference_markers.hmm GCF_014837145.1_ASM1483714v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:20,724] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:20,726] [INFO] Found 6/6 markers.
[2024-01-25 18:58:20,771] [INFO] Query marker FASTA was written to GCF_014837145.1_ASM1483714v1_genomic.fna/markers.fasta
[2024-01-25 18:58:20,771] [INFO] Task started: Blastn
[2024-01-25 18:58:20,771] [INFO] Running command: blastn -query GCF_014837145.1_ASM1483714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0af51296-d4a0-4983-9900-aaa4522f96f3/dqc_reference/reference_markers.fasta -out GCF_014837145.1_ASM1483714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:21,398] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:21,401] [INFO] Selected 22 target genomes.
[2024-01-25 18:58:21,401] [INFO] Target genome list was writen to GCF_014837145.1_ASM1483714v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:21,406] [INFO] Task started: fastANI
[2024-01-25 18:58:21,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg656bfae6-8a70-4301-9348-35609c9f4260/GCF_014837145.1_ASM1483714v1_genomic.fna.gz --refList GCF_014837145.1_ASM1483714v1_genomic.fna/target_genomes.txt --output GCF_014837145.1_ASM1483714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:38,917] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:38,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0af51296-d4a0-4983-9900-aaa4522f96f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:38,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0af51296-d4a0-4983-9900-aaa4522f96f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:38,930] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:38,931] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:38,931] [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 caseinilyticum	strain=GCR10	GCA_014837145.1	2771428	2771428	type	True	100.0	1424	1424	95	conclusive
Chryseobacterium piscicola	strain=DSM 21068	GCA_002943675.1	551459	551459	type	True	82.3348	803	1424	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	82.3146	824	1424	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	80.8761	708	1424	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	80.8297	708	1424	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.6087	685	1424	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	80.2418	637	1424	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	80.1355	637	1424	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.7712	652	1424	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	79.4824	566	1424	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	79.4793	577	1424	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	79.4288	569	1424	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	79.33	520	1424	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.313	575	1424	95	below_threshold
Chryseobacterium taihuense	strain=CGMCC 1.10941	GCA_900103755.1	1141221	1141221	type	True	79.262	494	1424	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	79.2013	550	1424	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	78.7827	464	1424	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	78.7154	482	1424	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	78.7055	471	1424	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	77.8225	313	1424	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	77.2158	183	1424	95	below_threshold
Kaistella treverensis	strain=DSM 22251	GCA_900114045.1	631455	631455	type	True	77.171	155	1424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:38,932] [INFO] DFAST Taxonomy check result was written to GCF_014837145.1_ASM1483714v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:38,933] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:38,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:38,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0af51296-d4a0-4983-9900-aaa4522f96f3/dqc_reference/checkm_data
[2024-01-25 18:58:38,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:38,977] [INFO] Task started: CheckM
[2024-01-25 18:58:38,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837145.1_ASM1483714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837145.1_ASM1483714v1_genomic.fna/checkm_input GCF_014837145.1_ASM1483714v1_genomic.fna/checkm_result
[2024-01-25 18:59:21,313] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:21,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:21,331] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:21,331] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:21,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837145.1_ASM1483714v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:21,332] [INFO] Task started: Blastn
[2024-01-25 18:59:21,332] [INFO] Running command: blastn -query GCF_014837145.1_ASM1483714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0af51296-d4a0-4983-9900-aaa4522f96f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837145.1_ASM1483714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:22,183] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:22,187] [INFO] Selected 15 target genomes.
[2024-01-25 18:59:22,187] [INFO] Target genome list was writen to GCF_014837145.1_ASM1483714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:22,198] [INFO] Task started: fastANI
[2024-01-25 18:59:22,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg656bfae6-8a70-4301-9348-35609c9f4260/GCF_014837145.1_ASM1483714v1_genomic.fna.gz --refList GCF_014837145.1_ASM1483714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837145.1_ASM1483714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:35,407] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:35,418] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:35,418] [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_014837145.1	s__Chryseobacterium caseinilyticum	100.0	1424	1424	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_001424105.1	s__Chryseobacterium sp001424105	94.639	1184	1424	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	84.8189	989	1424	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	82.3549	706	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.94	98.94	0.94	0.94	2	-
GCF_900156685.1	s__Chryseobacterium piscicola	82.3064	825	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003669035.1	s__Chryseobacterium sp003669035	81.4101	745	1424	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	80.831	707	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_014779605.1	s__Chryseobacterium sp014779605	80.6068	702	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
GCF_001507325.1	s__Chryseobacterium greenlandense	80.1469	636	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
GCF_900100115.1	s__Chryseobacterium soldanellicola	79.4795	577	1424	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	79.4246	570	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_900111495.1	s__Chryseobacterium wanjuense	79.3745	577	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103755.1	s__Chryseobacterium taihuense	79.2637	494	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.40	97.39	0.91	0.91	3	-
GCF_003663845.1	s__Chryseobacterium sp003663845	78.8374	496	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119445.1	s__Chryseobacterium sp004119445	78.8145	496	1424	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 18:59:35,425] [INFO] GTDB search result was written to GCF_014837145.1_ASM1483714v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:35,430] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:35,435] [INFO] DFAST_QC result json was written to GCF_014837145.1_ASM1483714v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:35,436] [INFO] DFAST_QC completed!
[2024-01-25 18:59:35,436] [INFO] Total running time: 0h1m30s