[2024-01-24 13:01:20,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:20,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:20,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d70e948-41e8-4581-99a7-6f733fa8d1a2/dqc_reference
[2024-01-24 13:01:21,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:21,766] [INFO] Task started: Prodigal
[2024-01-24 13:01:21,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b2b00f6-764e-4688-a488-d8f08032de50/GCF_030409875.1_ASM3040987v1_genomic.fna.gz | prodigal -d GCF_030409875.1_ASM3040987v1_genomic.fna/cds.fna -a GCF_030409875.1_ASM3040987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:41,826] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:41,827] [INFO] Task started: HMMsearch
[2024-01-24 13:01:41,827] [INFO] Running command: hmmsearch --tblout GCF_030409875.1_ASM3040987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d70e948-41e8-4581-99a7-6f733fa8d1a2/dqc_reference/reference_markers.hmm GCF_030409875.1_ASM3040987v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:42,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:42,144] [INFO] Found 6/6 markers.
[2024-01-24 13:01:42,198] [INFO] Query marker FASTA was written to GCF_030409875.1_ASM3040987v1_genomic.fna/markers.fasta
[2024-01-24 13:01:42,199] [INFO] Task started: Blastn
[2024-01-24 13:01:42,199] [INFO] Running command: blastn -query GCF_030409875.1_ASM3040987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d70e948-41e8-4581-99a7-6f733fa8d1a2/dqc_reference/reference_markers.fasta -out GCF_030409875.1_ASM3040987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:42,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:42,838] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:42,838] [INFO] Target genome list was writen to GCF_030409875.1_ASM3040987v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:42,844] [INFO] Task started: fastANI
[2024-01-24 13:01:42,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b2b00f6-764e-4688-a488-d8f08032de50/GCF_030409875.1_ASM3040987v1_genomic.fna.gz --refList GCF_030409875.1_ASM3040987v1_genomic.fna/target_genomes.txt --output GCF_030409875.1_ASM3040987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:57,712] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:57,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d70e948-41e8-4581-99a7-6f733fa8d1a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:57,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d70e948-41e8-4581-99a7-6f733fa8d1a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:57,727] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:57,727] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:57,727] [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	86.9077	1424	1877	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	86.8001	1419	1877	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	86.437	1358	1877	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	86.0325	1131	1877	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	85.9377	1260	1877	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	84.1646	1181	1877	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	84.1496	1167	1877	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	82.848	1141	1877	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	82.719	1141	1877	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3572	719	1877	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.2265	743	1877	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.3261	532	1877	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.287	607	1877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:57,729] [INFO] DFAST Taxonomy check result was written to GCF_030409875.1_ASM3040987v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:57,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:57,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:57,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d70e948-41e8-4581-99a7-6f733fa8d1a2/dqc_reference/checkm_data
[2024-01-24 13:01:57,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:57,791] [INFO] Task started: CheckM
[2024-01-24 13:01:57,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409875.1_ASM3040987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409875.1_ASM3040987v1_genomic.fna/checkm_input GCF_030409875.1_ASM3040987v1_genomic.fna/checkm_result
[2024-01-24 13:02:56,594] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:56,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:56,618] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:56,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:56,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409875.1_ASM3040987v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:56,619] [INFO] Task started: Blastn
[2024-01-24 13:02:56,619] [INFO] Running command: blastn -query GCF_030409875.1_ASM3040987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d70e948-41e8-4581-99a7-6f733fa8d1a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409875.1_ASM3040987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:57,472] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:57,477] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:57,477] [INFO] Target genome list was writen to GCF_030409875.1_ASM3040987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:57,488] [INFO] Task started: fastANI
[2024-01-24 13:02:57,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b2b00f6-764e-4688-a488-d8f08032de50/GCF_030409875.1_ASM3040987v1_genomic.fna.gz --refList GCF_030409875.1_ASM3040987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409875.1_ASM3040987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:13,452] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:13,467] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:03:13,468] [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_009900745.1	s__Chryseobacterium sp009900745	90.2979	1522	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815715.1	s__Chryseobacterium sp003815715	87.1552	1396	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637665.1	s__Chryseobacterium nakagawai	86.9179	1420	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385515.1	s__Chryseobacterium sp003385515	86.7939	1420	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_900078205.2	s__Chryseobacterium timonianum	86.467	1391	1877	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	86.4385	1357	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	86.306	1346	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829375.1	s__Chryseobacterium sp000829375	86.2294	1373	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684955.1	s__Chryseobacterium contaminans	86.0285	1132	1877	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004119455.1	s__Chryseobacterium sp004119455	85.9425	1330	1877	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	84.1822	1180	1877	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	82.8233	1161	1877	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 13:03:13,469] [INFO] GTDB search result was written to GCF_030409875.1_ASM3040987v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:13,470] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:13,473] [INFO] DFAST_QC result json was written to GCF_030409875.1_ASM3040987v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:13,473] [INFO] DFAST_QC completed!
[2024-01-24 13:03:13,473] [INFO] Total running time: 0h1m53s