[2024-01-24 14:31:28,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:28,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:28,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg8135f62c-460f-4c7d-bdf2-537a04034174/dqc_reference
[2024-01-24 14:31:29,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:29,898] [INFO] Task started: Prodigal
[2024-01-24 14:31:29,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg89796f8e-6f1c-4324-92b8-ee3ae991ac4e/GCF_002943655.1_ASM294365v1_genomic.fna.gz | prodigal -d GCF_002943655.1_ASM294365v1_genomic.fna/cds.fna -a GCF_002943655.1_ASM294365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:45,222] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:45,222] [INFO] Task started: HMMsearch
[2024-01-24 14:31:45,222] [INFO] Running command: hmmsearch --tblout GCF_002943655.1_ASM294365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8135f62c-460f-4c7d-bdf2-537a04034174/dqc_reference/reference_markers.hmm GCF_002943655.1_ASM294365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:45,447] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:45,448] [INFO] Found 6/6 markers.
[2024-01-24 14:31:45,486] [INFO] Query marker FASTA was written to GCF_002943655.1_ASM294365v1_genomic.fna/markers.fasta
[2024-01-24 14:31:45,486] [INFO] Task started: Blastn
[2024-01-24 14:31:45,486] [INFO] Running command: blastn -query GCF_002943655.1_ASM294365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8135f62c-460f-4c7d-bdf2-537a04034174/dqc_reference/reference_markers.fasta -out GCF_002943655.1_ASM294365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:47,243] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:47,246] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:47,246] [INFO] Target genome list was writen to GCF_002943655.1_ASM294365v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:47,249] [INFO] Task started: fastANI
[2024-01-24 14:31:47,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg89796f8e-6f1c-4324-92b8-ee3ae991ac4e/GCF_002943655.1_ASM294365v1_genomic.fna.gz --refList GCF_002943655.1_ASM294365v1_genomic.fna/target_genomes.txt --output GCF_002943655.1_ASM294365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:58,294] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:58,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8135f62c-460f-4c7d-bdf2-537a04034174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:58,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8135f62c-460f-4c7d-bdf2-537a04034174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:58,301] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:58,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:58,301] [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 shigense	strain=DSM 17126	GCA_002943655.1	297244	297244	type	True	100.0	1610	1612	95	conclusive
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	99.9917	1607	1612	95	conclusive
Chryseobacterium carnipullorum	strain=DSM 25581	GCA_900142785.1	1124835	1124835	type	True	91.5769	1363	1612	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	87.8771	1213	1612	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	86.2519	1242	1612	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	84.9326	1268	1612	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.4663	758	1612	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.298	629	1612	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.3177	583	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:58,303] [INFO] DFAST Taxonomy check result was written to GCF_002943655.1_ASM294365v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:58,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:58,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:58,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8135f62c-460f-4c7d-bdf2-537a04034174/dqc_reference/checkm_data
[2024-01-24 14:31:58,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:58,350] [INFO] Task started: CheckM
[2024-01-24 14:31:58,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002943655.1_ASM294365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002943655.1_ASM294365v1_genomic.fna/checkm_input GCF_002943655.1_ASM294365v1_genomic.fna/checkm_result
[2024-01-24 14:32:44,344] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:44,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:44,359] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:44,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:44,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002943655.1_ASM294365v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:44,360] [INFO] Task started: Blastn
[2024-01-24 14:32:44,360] [INFO] Running command: blastn -query GCF_002943655.1_ASM294365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8135f62c-460f-4c7d-bdf2-537a04034174/dqc_reference/reference_markers_gtdb.fasta -out GCF_002943655.1_ASM294365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:45,234] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:45,236] [INFO] Selected 8 target genomes.
[2024-01-24 14:32:45,237] [INFO] Target genome list was writen to GCF_002943655.1_ASM294365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:45,241] [INFO] Task started: fastANI
[2024-01-24 14:32:45,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg89796f8e-6f1c-4324-92b8-ee3ae991ac4e/GCF_002943655.1_ASM294365v1_genomic.fna.gz --refList GCF_002943655.1_ASM294365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002943655.1_ASM294365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:55,267] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:55,273] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:55,273] [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_900156575.1	s__Chryseobacterium shigense	99.9917	1607	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900142785.1	s__Chryseobacterium carnipullorum	91.5766	1363	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.36	98.32	0.90	0.88	5	-
GCF_012927325.1	s__Chryseobacterium antibioticum	87.8883	1212	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128945.1	s__Chryseobacterium sp900128945	86.2601	1276	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
GCF_900115055.1	s__Chryseobacterium oleae	86.2539	1242	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	86.229	1262	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754245.1	s__Chryseobacterium sp002754245	85.0503	1233	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737765.1	s__Chryseobacterium vrystaatense	84.9297	1269	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.86	98.86	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:55,274] [INFO] GTDB search result was written to GCF_002943655.1_ASM294365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:55,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:55,277] [INFO] DFAST_QC result json was written to GCF_002943655.1_ASM294365v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:55,277] [INFO] DFAST_QC completed!
[2024-01-24 14:32:55,277] [INFO] Total running time: 0h1m26s