[2024-01-25 19:01:35,716] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:35,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:35,718] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9c44fa8-6f48-46b8-94de-18c91bf7fa94/dqc_reference
[2024-01-25 19:01:36,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:36,908] [INFO] Task started: Prodigal
[2024-01-25 19:01:36,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4200970-3f3b-4891-b9d7-4731888d437f/GCF_009602705.1_ASM960270v1_genomic.fna.gz | prodigal -d GCF_009602705.1_ASM960270v1_genomic.fna/cds.fna -a GCF_009602705.1_ASM960270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:52,492] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:52,492] [INFO] Task started: HMMsearch
[2024-01-25 19:01:52,492] [INFO] Running command: hmmsearch --tblout GCF_009602705.1_ASM960270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9c44fa8-6f48-46b8-94de-18c91bf7fa94/dqc_reference/reference_markers.hmm GCF_009602705.1_ASM960270v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:52,752] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:52,753] [INFO] Found 6/6 markers.
[2024-01-25 19:01:52,794] [INFO] Query marker FASTA was written to GCF_009602705.1_ASM960270v1_genomic.fna/markers.fasta
[2024-01-25 19:01:52,795] [INFO] Task started: Blastn
[2024-01-25 19:01:52,795] [INFO] Running command: blastn -query GCF_009602705.1_ASM960270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9c44fa8-6f48-46b8-94de-18c91bf7fa94/dqc_reference/reference_markers.fasta -out GCF_009602705.1_ASM960270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:53,401] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:53,404] [INFO] Selected 26 target genomes.
[2024-01-25 19:01:53,404] [INFO] Target genome list was writen to GCF_009602705.1_ASM960270v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:53,413] [INFO] Task started: fastANI
[2024-01-25 19:01:53,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4200970-3f3b-4891-b9d7-4731888d437f/GCF_009602705.1_ASM960270v1_genomic.fna.gz --refList GCF_009602705.1_ASM960270v1_genomic.fna/target_genomes.txt --output GCF_009602705.1_ASM960270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:18,922] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:18,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9c44fa8-6f48-46b8-94de-18c91bf7fa94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:18,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9c44fa8-6f48-46b8-94de-18c91bf7fa94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:18,937] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:18,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:18,938] [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 vaccae	strain=CA7	GCA_009602705.1	2604424	2604424	type	True	100.0	1705	1708	95	conclusive
Chryseobacterium endalhagicum	strain=L7	GCA_016745235.1	2797638	2797638	type	True	81.9709	971	1708	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	81.9538	959	1708	95	below_threshold
Chryseobacterium elymi	strain=KCTC 22547	GCA_003385495.1	395936	395936	type	True	81.7466	902	1708	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	81.7394	990	1708	95	below_threshold
Chryseobacterium lathyri	strain=NBRC 105250	GCA_007991435.1	395933	395933	type	True	81.7025	904	1708	95	below_threshold
Chryseobacterium carnipullorum	strain=DSM 25581	GCA_900142785.1	1124835	1124835	type	True	81.6784	929	1708	95	below_threshold
Chryseobacterium lathyri	strain=KCTC 22544	GCA_003290185.1	395933	395933	type	True	81.6665	920	1708	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	81.6649	949	1708	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	81.6508	974	1708	95	below_threshold
Chryseobacterium kwangjuense	strain=KJ1R5	GCA_001563495.1	267125	267125	type	True	81.614	978	1708	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	81.5805	934	1708	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	81.5733	959	1708	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	81.5431	840	1708	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	81.4423	905	1708	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	81.3934	918	1708	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	81.3453	959	1708	95	below_threshold
Chryseobacterium indologenes	strain=NCTC10796	GCA_900460995.1	253	253	type	True	81.2812	863	1708	95	below_threshold
Chryseobacterium indologenes	strain=NBRC 14944	GCA_000520835.1	253	253	type	True	81.2312	845	1708	95	below_threshold
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	81.1842	886	1708	95	below_threshold
Chryseobacterium indologenes	strain=DSM 16777	GCA_900113975.1	253	253	type	True	81.1796	845	1708	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.5133	694	1708	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.4915	685	1708	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.3248	737	1708	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	76.9047	109	1708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:18,939] [INFO] DFAST Taxonomy check result was written to GCF_009602705.1_ASM960270v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:18,939] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:18,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:18,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9c44fa8-6f48-46b8-94de-18c91bf7fa94/dqc_reference/checkm_data
[2024-01-25 19:02:18,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:18,990] [INFO] Task started: CheckM
[2024-01-25 19:02:18,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009602705.1_ASM960270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009602705.1_ASM960270v1_genomic.fna/checkm_input GCF_009602705.1_ASM960270v1_genomic.fna/checkm_result
[2024-01-25 19:03:05,567] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:05,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:05,585] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:05,585] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:05,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009602705.1_ASM960270v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:05,586] [INFO] Task started: Blastn
[2024-01-25 19:03:05,586] [INFO] Running command: blastn -query GCF_009602705.1_ASM960270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9c44fa8-6f48-46b8-94de-18c91bf7fa94/dqc_reference/reference_markers_gtdb.fasta -out GCF_009602705.1_ASM960270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:06,427] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:06,430] [INFO] Selected 18 target genomes.
[2024-01-25 19:03:06,430] [INFO] Target genome list was writen to GCF_009602705.1_ASM960270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:06,450] [INFO] Task started: fastANI
[2024-01-25 19:03:06,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4200970-3f3b-4891-b9d7-4731888d437f/GCF_009602705.1_ASM960270v1_genomic.fna.gz --refList GCF_009602705.1_ASM960270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009602705.1_ASM960270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:26,795] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:26,806] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:26,807] [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_009602705.1	s__Chryseobacterium vaccae	100.0	1708	1708	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_001295265.1	s__Chryseobacterium indologenes_A	89.6388	1355	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002439165.1	s__Chryseobacterium indologenes_E	87.2443	1333	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745235.1	s__Chryseobacterium sp016745235	81.9836	969	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207845.1	s__Chryseobacterium shigense_A	81.9728	868	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001045465.1	s__Chryseobacterium angstadtii	81.9434	960	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385495.1	s__Chryseobacterium elymi	81.7385	903	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	81.7359	995	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142785.1	s__Chryseobacterium carnipullorum	81.6846	928	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.36	98.32	0.90	0.88	5	-
GCF_003290185.1	s__Chryseobacterium lathyri	81.6638	920	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001563495.1	s__Chryseobacterium kwangjuense	81.6032	979	1708	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	81.5833	957	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_000829375.1	s__Chryseobacterium sp000829375	81.534	944	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001013295.1	s__Chryseobacterium indologenes_B	81.4349	983	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.53	97.53	0.94	0.90	6	-
GCF_011752975.1	s__Chryseobacterium sp011752975	81.3987	920	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119455.1	s__Chryseobacterium sp004119455	81.3824	942	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002899945.2	s__Chryseobacterium viscerum	81.3464	958	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.88	95.74	0.91	0.87	3	-
GCA_016025055.1	s__Chryseobacterium indologenes	81.2892	859	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.10	98.65	0.93	0.89	60	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:26,808] [INFO] GTDB search result was written to GCF_009602705.1_ASM960270v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:26,808] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:26,813] [INFO] DFAST_QC result json was written to GCF_009602705.1_ASM960270v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:26,814] [INFO] DFAST_QC completed!
[2024-01-25 19:03:26,814] [INFO] Total running time: 0h1m51s