[2024-01-24 11:44:05,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,462] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd1c69c2-723d-41c5-a512-9b3a9e77cbcd/dqc_reference
[2024-01-24 11:44:08,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,841] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc95df9-ad31-42b0-a8a8-265c6daeb4de/GCF_003385415.1_ASM338541v1_genomic.fna.gz | prodigal -d GCF_003385415.1_ASM338541v1_genomic.fna/cds.fna -a GCF_003385415.1_ASM338541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:23,190] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:23,191] [INFO] Task started: HMMsearch
[2024-01-24 11:44:23,191] [INFO] Running command: hmmsearch --tblout GCF_003385415.1_ASM338541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd1c69c2-723d-41c5-a512-9b3a9e77cbcd/dqc_reference/reference_markers.hmm GCF_003385415.1_ASM338541v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:23,464] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:23,466] [INFO] Found 6/6 markers.
[2024-01-24 11:44:23,504] [INFO] Query marker FASTA was written to GCF_003385415.1_ASM338541v1_genomic.fna/markers.fasta
[2024-01-24 11:44:23,505] [INFO] Task started: Blastn
[2024-01-24 11:44:23,505] [INFO] Running command: blastn -query GCF_003385415.1_ASM338541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd1c69c2-723d-41c5-a512-9b3a9e77cbcd/dqc_reference/reference_markers.fasta -out GCF_003385415.1_ASM338541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:24,144] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:24,148] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:24,148] [INFO] Target genome list was writen to GCF_003385415.1_ASM338541v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:24,153] [INFO] Task started: fastANI
[2024-01-24 11:44:24,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc95df9-ad31-42b0-a8a8-265c6daeb4de/GCF_003385415.1_ASM338541v1_genomic.fna.gz --refList GCF_003385415.1_ASM338541v1_genomic.fna/target_genomes.txt --output GCF_003385415.1_ASM338541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:35,769] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:35,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd1c69c2-723d-41c5-a512-9b3a9e77cbcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:35,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd1c69c2-723d-41c5-a512-9b3a9e77cbcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:35,791] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:35,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:35,792] [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 piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	100.0	1355	1364	95	conclusive
Chryseobacterium balustinum	strain=DSM 16775	GCA_900168205.1	246	246	type	True	94.1369	1128	1364	95	below_threshold
Chryseobacterium balustinum	strain=NCTC11212	GCA_900446785.1	246	246	type	True	94.0892	1060	1364	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	91.016	1133	1364	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	90.8116	1108	1364	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	90.4983	1073	1364	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	90.4354	1075	1364	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	89.9316	1104	1364	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	81.4374	766	1364	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.7767	659	1364	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.6729	731	1364	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.7183	433	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,794] [INFO] DFAST Taxonomy check result was written to GCF_003385415.1_ASM338541v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:35,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:35,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:35,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd1c69c2-723d-41c5-a512-9b3a9e77cbcd/dqc_reference/checkm_data
[2024-01-24 11:44:35,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:35,837] [INFO] Task started: CheckM
[2024-01-24 11:44:35,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385415.1_ASM338541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385415.1_ASM338541v1_genomic.fna/checkm_input GCF_003385415.1_ASM338541v1_genomic.fna/checkm_result
[2024-01-24 11:45:20,481] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:20,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:20,498] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:20,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:20,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385415.1_ASM338541v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:20,499] [INFO] Task started: Blastn
[2024-01-24 11:45:20,499] [INFO] Running command: blastn -query GCF_003385415.1_ASM338541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd1c69c2-723d-41c5-a512-9b3a9e77cbcd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385415.1_ASM338541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:21,372] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:21,376] [INFO] Selected 9 target genomes.
[2024-01-24 11:45:21,377] [INFO] Target genome list was writen to GCF_003385415.1_ASM338541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:21,386] [INFO] Task started: fastANI
[2024-01-24 11:45:21,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc95df9-ad31-42b0-a8a8-265c6daeb4de/GCF_003385415.1_ASM338541v1_genomic.fna.gz --refList GCF_003385415.1_ASM338541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385415.1_ASM338541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:30,031] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:30,045] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:30,045] [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_003385415.1	s__Chryseobacterium piscium	100.0	1355	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.69	96.60	0.88	0.87	3	conclusive
GCF_900168205.1	s__Chryseobacterium balustinum	94.1369	1128	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.96	99.93	0.98	0.95	3	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	91.0197	1133	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
GCF_006175945.1	s__Chryseobacterium mulctrae	90.8116	1108	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815915.1	s__Chryseobacterium indoltheticum	90.4354	1075	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_001677955.1	s__Chryseobacterium sp001677955	90.0464	1081	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_903166575.1	s__Chryseobacterium sp903166575	89.945	1103	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779605.1	s__Chryseobacterium sp014779605	88.6929	1064	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:30,047] [INFO] GTDB search result was written to GCF_003385415.1_ASM338541v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:30,047] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:30,050] [INFO] DFAST_QC result json was written to GCF_003385415.1_ASM338541v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:30,050] [INFO] DFAST_QC completed!
[2024-01-24 11:45:30,051] [INFO] Total running time: 0h1m25s