[2024-01-25 18:55:36,030] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:36,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:36,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe143e98-771f-46f4-b39a-7d9217d1557f/dqc_reference
[2024-01-25 18:55:37,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:37,246] [INFO] Task started: Prodigal
[2024-01-25 18:55:37,246] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b16c5c9-a3f7-4328-8aa3-d4b041a56084/GCF_024807225.1_ASM2480722v1_genomic.fna.gz | prodigal -d GCF_024807225.1_ASM2480722v1_genomic.fna/cds.fna -a GCF_024807225.1_ASM2480722v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:52,022] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:52,022] [INFO] Task started: HMMsearch
[2024-01-25 18:55:52,022] [INFO] Running command: hmmsearch --tblout GCF_024807225.1_ASM2480722v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe143e98-771f-46f4-b39a-7d9217d1557f/dqc_reference/reference_markers.hmm GCF_024807225.1_ASM2480722v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:52,276] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:52,278] [INFO] Found 6/6 markers.
[2024-01-25 18:55:52,319] [INFO] Query marker FASTA was written to GCF_024807225.1_ASM2480722v1_genomic.fna/markers.fasta
[2024-01-25 18:55:52,320] [INFO] Task started: Blastn
[2024-01-25 18:55:52,320] [INFO] Running command: blastn -query GCF_024807225.1_ASM2480722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe143e98-771f-46f4-b39a-7d9217d1557f/dqc_reference/reference_markers.fasta -out GCF_024807225.1_ASM2480722v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:52,943] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:52,946] [INFO] Selected 16 target genomes.
[2024-01-25 18:55:52,946] [INFO] Target genome list was writen to GCF_024807225.1_ASM2480722v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:52,956] [INFO] Task started: fastANI
[2024-01-25 18:55:52,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b16c5c9-a3f7-4328-8aa3-d4b041a56084/GCF_024807225.1_ASM2480722v1_genomic.fna.gz --refList GCF_024807225.1_ASM2480722v1_genomic.fna/target_genomes.txt --output GCF_024807225.1_ASM2480722v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:10,281] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:10,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe143e98-771f-46f4-b39a-7d9217d1557f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:10,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe143e98-771f-46f4-b39a-7d9217d1557f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:10,292] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:10,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:10,292] [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 ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	100.0	1571	1572	95	conclusive
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	83.6682	1035	1572	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	83.2594	966	1572	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	83.1651	991	1572	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	83.1229	1038	1572	95	below_threshold
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	83.0463	1042	1572	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	82.5382	797	1572	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	82.2944	910	1572	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	82.2859	974	1572	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	82.2244	952	1572	95	below_threshold
Chryseobacterium polytrichastri	strain=DSM 26899	GCA_900142445.1	1302687	1302687	type	True	81.923	952	1572	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	81.1522	800	1572	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	81.1374	810	1572	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	80.826	741	1572	95	below_threshold
Chryseobacterium caseinilyticum	strain=GCR10	GCA_014837145.1	2771428	2771428	type	True	79.7666	670	1572	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.2944	523	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:10,293] [INFO] DFAST Taxonomy check result was written to GCF_024807225.1_ASM2480722v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:10,294] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:10,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:10,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe143e98-771f-46f4-b39a-7d9217d1557f/dqc_reference/checkm_data
[2024-01-25 18:56:10,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:10,341] [INFO] Task started: CheckM
[2024-01-25 18:56:10,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024807225.1_ASM2480722v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024807225.1_ASM2480722v1_genomic.fna/checkm_input GCF_024807225.1_ASM2480722v1_genomic.fna/checkm_result
[2024-01-25 18:56:53,860] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:53,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:53,881] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:53,881] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:53,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024807225.1_ASM2480722v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:53,882] [INFO] Task started: Blastn
[2024-01-25 18:56:53,882] [INFO] Running command: blastn -query GCF_024807225.1_ASM2480722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe143e98-771f-46f4-b39a-7d9217d1557f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024807225.1_ASM2480722v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:54,778] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:54,780] [INFO] Selected 18 target genomes.
[2024-01-25 18:56:54,780] [INFO] Target genome list was writen to GCF_024807225.1_ASM2480722v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:54,795] [INFO] Task started: fastANI
[2024-01-25 18:56:54,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b16c5c9-a3f7-4328-8aa3-d4b041a56084/GCF_024807225.1_ASM2480722v1_genomic.fna.gz --refList GCF_024807225.1_ASM2480722v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024807225.1_ASM2480722v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:14,287] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:14,299] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:57:14,299] [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_000799195.1	s__Chryseobacterium sp000799195	88.6412	1172	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425355.1	s__Chryseobacterium sp001425355	83.7359	1027	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	83.6699	1035	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456155.1	s__Chryseobacterium sp001456155	83.3123	940	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_003815655.1	s__Chryseobacterium sp003815655	83.2002	993	1572	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	83.1502	993	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129245.1	s__Chryseobacterium arachidis	83.1189	1039	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648155.1	s__Chryseobacterium glaciei	83.0702	1042	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813825.1	s__Chryseobacterium taiwanense	82.4836	903	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	82.4109	937	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045455.1	s__Chryseobacterium sp001045455	82.3695	853	1572	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	82.294	973	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_002177115.1	s__Chryseobacterium mucoviscidosis	82.2541	948	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCF_000430825.1	s__Chryseobacterium daeguense	82.2115	927	1572	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	81.9258	952	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099685.1	s__Chryseobacterium taeanense	81.1266	811	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424105.1	s__Chryseobacterium sp001424105	79.8308	652	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837145.1	s__Chryseobacterium caseinilyticum	79.7777	669	1572	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 18:57:14,300] [INFO] GTDB search result was written to GCF_024807225.1_ASM2480722v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:14,301] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:14,304] [INFO] DFAST_QC result json was written to GCF_024807225.1_ASM2480722v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:14,304] [INFO] DFAST_QC completed!
[2024-01-25 18:57:14,304] [INFO] Total running time: 0h1m38s