[2024-01-24 12:44:10,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg225eeaf5-c838-4288-844d-3b42033c7c62/dqc_reference
[2024-01-24 12:44:12,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,359] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,359] [INFO] Running command: gunzip -c /var/lib/cwl/stg268101e9-b2d9-4ed1-bc7f-a71cbbbbc7fb/GCF_900460995.1_42552_F01_genomic.fna.gz | prodigal -d GCF_900460995.1_42552_F01_genomic.fna/cds.fna -a GCF_900460995.1_42552_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:31,413] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:31,413] [INFO] Task started: HMMsearch
[2024-01-24 12:44:31,413] [INFO] Running command: hmmsearch --tblout GCF_900460995.1_42552_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg225eeaf5-c838-4288-844d-3b42033c7c62/dqc_reference/reference_markers.hmm GCF_900460995.1_42552_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:31,773] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:31,774] [INFO] Found 6/6 markers.
[2024-01-24 12:44:31,816] [INFO] Query marker FASTA was written to GCF_900460995.1_42552_F01_genomic.fna/markers.fasta
[2024-01-24 12:44:31,817] [INFO] Task started: Blastn
[2024-01-24 12:44:31,817] [INFO] Running command: blastn -query GCF_900460995.1_42552_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg225eeaf5-c838-4288-844d-3b42033c7c62/dqc_reference/reference_markers.fasta -out GCF_900460995.1_42552_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:32,455] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:32,459] [INFO] Selected 15 target genomes.
[2024-01-24 12:44:32,459] [INFO] Target genome list was writen to GCF_900460995.1_42552_F01_genomic.fna/target_genomes.txt
[2024-01-24 12:44:32,487] [INFO] Task started: fastANI
[2024-01-24 12:44:32,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg268101e9-b2d9-4ed1-bc7f-a71cbbbbc7fb/GCF_900460995.1_42552_F01_genomic.fna.gz --refList GCF_900460995.1_42552_F01_genomic.fna/target_genomes.txt --output GCF_900460995.1_42552_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:48,789] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:48,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg225eeaf5-c838-4288-844d-3b42033c7c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:48,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg225eeaf5-c838-4288-844d-3b42033c7c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:48,802] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:44:48,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:48,802] [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 indologenes	strain=NCTC10796	GCA_900460995.1	253	253	type	True	100.0	1641	1642	95	conclusive
Chryseobacterium indologenes	strain=DSM 16777	GCA_900113975.1	253	253	type	True	99.9982	1619	1642	95	conclusive
Chryseobacterium indologenes	strain=NBRC 14944	GCA_000520835.1	253	253	type	True	99.9876	1564	1642	95	conclusive
Chryseobacterium phosphatilyticum	strain=ISE14	GCA_002899825.2	475075	475075	type	True	85.6456	1299	1642	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	84.2989	1241	1642	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	83.1084	1063	1642	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	82.9604	1030	1642	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	82.905	1006	1642	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	82.4833	1051	1642	95	below_threshold
Chryseobacterium vaccae	strain=CA7	GCA_009602705.1	2604424	2604424	type	True	81.3883	844	1642	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.2917	652	1642	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.2128	686	1642	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.082	708	1642	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.1778	491	1642	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	78.8972	579	1642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:48,804] [INFO] DFAST Taxonomy check result was written to GCF_900460995.1_42552_F01_genomic.fna/tc_result.tsv
[2024-01-24 12:44:48,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:48,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:48,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg225eeaf5-c838-4288-844d-3b42033c7c62/dqc_reference/checkm_data
[2024-01-24 12:44:48,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:48,858] [INFO] Task started: CheckM
[2024-01-24 12:44:48,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460995.1_42552_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460995.1_42552_F01_genomic.fna/checkm_input GCF_900460995.1_42552_F01_genomic.fna/checkm_result
[2024-01-24 12:45:46,215] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:46,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,239] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:46,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:46,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460995.1_42552_F01_genomic.fna/markers.fasta)
[2024-01-24 12:45:46,240] [INFO] Task started: Blastn
[2024-01-24 12:45:46,240] [INFO] Running command: blastn -query GCF_900460995.1_42552_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg225eeaf5-c838-4288-844d-3b42033c7c62/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460995.1_42552_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:47,092] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:47,096] [INFO] Selected 18 target genomes.
[2024-01-24 12:45:47,096] [INFO] Target genome list was writen to GCF_900460995.1_42552_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:47,113] [INFO] Task started: fastANI
[2024-01-24 12:45:47,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg268101e9-b2d9-4ed1-bc7f-a71cbbbbc7fb/GCF_900460995.1_42552_F01_genomic.fna.gz --refList GCF_900460995.1_42552_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460995.1_42552_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:06,608] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:06,637] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:06,638] [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
GCA_016025055.1	s__Chryseobacterium indologenes	99.9765	1636	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.10	98.65	0.93	0.89	60	conclusive
GCF_002899825.2	s__Chryseobacterium phosphatilyticum	85.6603	1298	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815875.1	s__Chryseobacterium lactis	84.3373	1251	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002835665.1	s__Chryseobacterium sp002835665	83.3523	882	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386505.1	s__Chryseobacterium sediminis	82.9753	1043	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	82.9687	1029	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_000799235.1	s__Chryseobacterium sp000799235	82.8568	1052	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916905.1	s__Chryseobacterium candidae	82.8417	974	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.64	98.56	0.91	0.91	3	-
GCF_000829375.1	s__Chryseobacterium sp000829375	82.8415	1042	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979755.1	s__Chryseobacterium culicis_A	82.8161	1050	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_000799335.1	s__Chryseobacterium sp000799335	82.7835	1064	1642	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	82.7621	1020	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663845.1	s__Chryseobacterium sp003663845	82.7177	1032	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979455.1	s__Chryseobacterium sp002979455	82.6699	1037	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385515.1	s__Chryseobacterium sp003385515	82.624	1037	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	82.6031	1018	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899945.2	s__Chryseobacterium viscerum	82.4837	1051	1642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.88	95.74	0.91	0.87	3	-
GCF_009602705.1	s__Chryseobacterium vaccae	81.3956	844	1642	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 12:46:06,640] [INFO] GTDB search result was written to GCF_900460995.1_42552_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:06,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:06,645] [INFO] DFAST_QC result json was written to GCF_900460995.1_42552_F01_genomic.fna/dqc_result.json
[2024-01-24 12:46:06,645] [INFO] DFAST_QC completed!
[2024-01-24 12:46:06,645] [INFO] Total running time: 0h1m56s