[2024-01-25 20:01:05,851] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:05,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:05,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdeb655f-8b7a-4e85-abd6-da63b24fa69b/dqc_reference
[2024-01-25 20:01:06,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:06,963] [INFO] Task started: Prodigal
[2024-01-25 20:01:06,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg53acfaa6-2756-41b5-b49d-9dd9d01efd2a/GCF_000401415.1_ASM40141v1_genomic.fna.gz | prodigal -d GCF_000401415.1_ASM40141v1_genomic.fna/cds.fna -a GCF_000401415.1_ASM40141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:17,607] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:17,608] [INFO] Task started: HMMsearch
[2024-01-25 20:01:17,608] [INFO] Running command: hmmsearch --tblout GCF_000401415.1_ASM40141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdeb655f-8b7a-4e85-abd6-da63b24fa69b/dqc_reference/reference_markers.hmm GCF_000401415.1_ASM40141v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:17,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:17,824] [INFO] Found 6/6 markers.
[2024-01-25 20:01:17,853] [INFO] Query marker FASTA was written to GCF_000401415.1_ASM40141v1_genomic.fna/markers.fasta
[2024-01-25 20:01:17,853] [INFO] Task started: Blastn
[2024-01-25 20:01:17,853] [INFO] Running command: blastn -query GCF_000401415.1_ASM40141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdeb655f-8b7a-4e85-abd6-da63b24fa69b/dqc_reference/reference_markers.fasta -out GCF_000401415.1_ASM40141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:18,450] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:18,452] [INFO] Selected 15 target genomes.
[2024-01-25 20:01:18,452] [INFO] Target genome list was writen to GCF_000401415.1_ASM40141v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:18,468] [INFO] Task started: fastANI
[2024-01-25 20:01:18,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg53acfaa6-2756-41b5-b49d-9dd9d01efd2a/GCF_000401415.1_ASM40141v1_genomic.fna.gz --refList GCF_000401415.1_ASM40141v1_genomic.fna/target_genomes.txt --output GCF_000401415.1_ASM40141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:29,593] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:29,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdeb655f-8b7a-4e85-abd6-da63b24fa69b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:29,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdeb655f-8b7a-4e85-abd6-da63b24fa69b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:29,604] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:01:29,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:29,604] [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
Elizabethkingia meningoseptica	strain=ATCC 13253	GCA_000401415.1	238	238	type	True	100.0	1204	1209	95	conclusive
Elizabethkingia meningoseptica	strain=NCTC10016	GCA_900475375.1	238	238	type	True	99.9911	1209	1209	95	conclusive
Elizabethkingia meningoseptica	strain=NBRC 12535	GCA_000367325.1	238	238	type	True	99.9853	1187	1209	95	conclusive
Elizabethkingia miricola	strain=GTC_862	GCA_001675285.1	172045	172045	type	True	81.8795	799	1209	95	below_threshold
Elizabethkingia anophelis	strain=R26	GCA_000331815.1	1117645	1117645	type	True	81.8161	779	1209	95	below_threshold
Elizabethkingia occulta	strain=G4070	GCA_002023715.1	1867263	1867263	type	True	81.8102	813	1209	95	below_threshold
Elizabethkingia miricola	strain=DSM 14571	GCA_008124555.1	172045	172045	type	True	81.8047	820	1209	95	below_threshold
Elizabethkingia ursingii	strain=G4122	GCA_001521765.1	1756150	1756150	type	True	81.7797	813	1209	95	below_threshold
Chryseobacterium camelliae	strain=Dolsongi-HT1	GCA_002770595.1	1265445	1265445	type	True	77.6745	120	1209	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	77.2073	168	1209	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.0045	105	1209	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.0045	105	1209	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	76.9321	68	1209	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	76.9087	192	1209	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	75.1894	50	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:29,605] [INFO] DFAST Taxonomy check result was written to GCF_000401415.1_ASM40141v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:29,606] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:29,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:29,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdeb655f-8b7a-4e85-abd6-da63b24fa69b/dqc_reference/checkm_data
[2024-01-25 20:01:29,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:29,649] [INFO] Task started: CheckM
[2024-01-25 20:01:29,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000401415.1_ASM40141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000401415.1_ASM40141v1_genomic.fna/checkm_input GCF_000401415.1_ASM40141v1_genomic.fna/checkm_result
[2024-01-25 20:02:03,059] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:03,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:03,075] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:03,076] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:03,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000401415.1_ASM40141v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:03,076] [INFO] Task started: Blastn
[2024-01-25 20:02:03,076] [INFO] Running command: blastn -query GCF_000401415.1_ASM40141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdeb655f-8b7a-4e85-abd6-da63b24fa69b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000401415.1_ASM40141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:03,988] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:03,990] [INFO] Selected 11 target genomes.
[2024-01-25 20:02:03,990] [INFO] Target genome list was writen to GCF_000401415.1_ASM40141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:04,008] [INFO] Task started: fastANI
[2024-01-25 20:02:04,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg53acfaa6-2756-41b5-b49d-9dd9d01efd2a/GCF_000401415.1_ASM40141v1_genomic.fna.gz --refList GCF_000401415.1_ASM40141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000401415.1_ASM40141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:12,976] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:12,983] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:12,983] [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_000367325.1	s__Elizabethkingia meningoseptica	99.9853	1187	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.78	98.42	0.95	0.93	51	conclusive
GCF_001675285.1	s__Elizabethkingia miricola	81.8791	799	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.66	96.19	0.91	0.86	23	-
GCF_002023665.2	s__Elizabethkingia anophelis	81.8325	783	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.27	97.37	0.90	0.86	104	-
GCF_002023715.1	s__Elizabethkingia occulta	81.8104	813	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	99.55	99.55	0.94	0.94	2	-
GCF_001521765.1	s__Elizabethkingia ursingii	81.781	812	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.28	97.02	0.89	0.88	5	-
GCF_002024805.1	s__Elizabethkingia bruuniana	81.6931	798	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.72	96.90	0.94	0.86	13	-
GCF_003058195.1	s__Elizabethkingia sp003058195	81.6647	831	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002770595.1	s__Chryseobacterium camelliae	77.6556	119	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100115.1	s__Chryseobacterium soldanellicola	77.2074	168	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728305.1	s__Chryseobacterium sp902728305	77.0819	147	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000799255.1	s__Chryseobacterium sp000799255	76.9603	149	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.94	98.94	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:12,985] [INFO] GTDB search result was written to GCF_000401415.1_ASM40141v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:12,985] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:12,988] [INFO] DFAST_QC result json was written to GCF_000401415.1_ASM40141v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:12,988] [INFO] DFAST_QC completed!
[2024-01-25 20:02:12,988] [INFO] Total running time: 0h1m7s