[2024-01-24 13:50:25,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:25,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:25,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg909f4398-07c7-467d-8937-00b099d9789e/dqc_reference
[2024-01-24 13:50:27,054] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,055] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,055] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d2fcb30-8127-444e-b99b-8076bc0b4324/GCF_900637665.1_52437_G01_genomic.fna.gz | prodigal -d GCF_900637665.1_52437_G01_genomic.fna/cds.fna -a GCF_900637665.1_52437_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:47,064] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:47,065] [INFO] Task started: HMMsearch
[2024-01-24 13:50:47,065] [INFO] Running command: hmmsearch --tblout GCF_900637665.1_52437_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg909f4398-07c7-467d-8937-00b099d9789e/dqc_reference/reference_markers.hmm GCF_900637665.1_52437_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:47,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:47,360] [INFO] Found 6/6 markers.
[2024-01-24 13:50:47,406] [INFO] Query marker FASTA was written to GCF_900637665.1_52437_G01_genomic.fna/markers.fasta
[2024-01-24 13:50:47,406] [INFO] Task started: Blastn
[2024-01-24 13:50:47,406] [INFO] Running command: blastn -query GCF_900637665.1_52437_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg909f4398-07c7-467d-8937-00b099d9789e/dqc_reference/reference_markers.fasta -out GCF_900637665.1_52437_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:48,047] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:48,051] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:48,052] [INFO] Target genome list was writen to GCF_900637665.1_52437_G01_genomic.fna/target_genomes.txt
[2024-01-24 13:50:48,101] [INFO] Task started: fastANI
[2024-01-24 13:50:48,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2fcb30-8127-444e-b99b-8076bc0b4324/GCF_900637665.1_52437_G01_genomic.fna.gz --refList GCF_900637665.1_52437_G01_genomic.fna/target_genomes.txt --output GCF_900637665.1_52437_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:03,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:03,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg909f4398-07c7-467d-8937-00b099d9789e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:03,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg909f4398-07c7-467d-8937-00b099d9789e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:03,371] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:51:03,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:03,371] [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 nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	100.0	1865	1867	95	conclusive
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	87.2552	1375	1867	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	87.1488	1362	1867	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	86.8602	1101	1867	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	86.744	1234	1867	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	84.3207	1210	1867	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	84.2965	1168	1867	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	83.2583	1103	1867	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	82.9838	1120	1867	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.6334	689	1867	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.6042	682	1867	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.4271	742	1867	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.8318	527	1867	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.345	615	1867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:03,373] [INFO] DFAST Taxonomy check result was written to GCF_900637665.1_52437_G01_genomic.fna/tc_result.tsv
[2024-01-24 13:51:03,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:03,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:03,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg909f4398-07c7-467d-8937-00b099d9789e/dqc_reference/checkm_data
[2024-01-24 13:51:03,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:03,430] [INFO] Task started: CheckM
[2024-01-24 13:51:03,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637665.1_52437_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637665.1_52437_G01_genomic.fna/checkm_input GCF_900637665.1_52437_G01_genomic.fna/checkm_result
[2024-01-24 13:52:01,617] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:01,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:01,640] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:01,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:01,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637665.1_52437_G01_genomic.fna/markers.fasta)
[2024-01-24 13:52:01,641] [INFO] Task started: Blastn
[2024-01-24 13:52:01,641] [INFO] Running command: blastn -query GCF_900637665.1_52437_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg909f4398-07c7-467d-8937-00b099d9789e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637665.1_52437_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:02,513] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:02,517] [INFO] Selected 11 target genomes.
[2024-01-24 13:52:02,518] [INFO] Target genome list was writen to GCF_900637665.1_52437_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:02,546] [INFO] Task started: fastANI
[2024-01-24 13:52:02,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2fcb30-8127-444e-b99b-8076bc0b4324/GCF_900637665.1_52437_G01_genomic.fna.gz --refList GCF_900637665.1_52437_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637665.1_52437_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:16,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:16,622] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:16,623] [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_900637665.1	s__Chryseobacterium nakagawai	100.0	1865	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003815715.1	s__Chryseobacterium sp003815715	94.8486	1523	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218825.1	s__Chryseobacterium bernardetii	87.8455	1395	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.97	99.97	0.99	0.99	3	-
GCF_900078205.2	s__Chryseobacterium timonianum	87.7408	1390	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	87.3803	1333	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100075.1	s__Chryseobacterium jejuense	87.2552	1375	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003385515.1	s__Chryseobacterium sp003385515	87.1707	1358	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_000829375.1	s__Chryseobacterium sp000829375	87.1321	1361	1867	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	86.9655	1327	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	84.3189	1210	1867	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	83.024	1139	1867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:16,625] [INFO] GTDB search result was written to GCF_900637665.1_52437_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:16,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:16,629] [INFO] DFAST_QC result json was written to GCF_900637665.1_52437_G01_genomic.fna/dqc_result.json
[2024-01-24 13:52:16,629] [INFO] DFAST_QC completed!
[2024-01-24 13:52:16,629] [INFO] Total running time: 0h1m51s