[2024-01-25 20:22:50,559] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg488ef193-287c-4eac-bd5b-5050fd7ceafa/dqc_reference
[2024-01-25 20:22:51,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,725] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg2050adf1-9f08-4a4a-be4d-8742f896ed40/GCF_014635525.1_ASM1463552v1_genomic.fna.gz | prodigal -d GCF_014635525.1_ASM1463552v1_genomic.fna/cds.fna -a GCF_014635525.1_ASM1463552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:07,191] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:07,192] [INFO] Task started: HMMsearch
[2024-01-25 20:23:07,192] [INFO] Running command: hmmsearch --tblout GCF_014635525.1_ASM1463552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg488ef193-287c-4eac-bd5b-5050fd7ceafa/dqc_reference/reference_markers.hmm GCF_014635525.1_ASM1463552v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:07,477] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:07,478] [INFO] Found 6/6 markers.
[2024-01-25 20:23:07,515] [INFO] Query marker FASTA was written to GCF_014635525.1_ASM1463552v1_genomic.fna/markers.fasta
[2024-01-25 20:23:07,516] [INFO] Task started: Blastn
[2024-01-25 20:23:07,516] [INFO] Running command: blastn -query GCF_014635525.1_ASM1463552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg488ef193-287c-4eac-bd5b-5050fd7ceafa/dqc_reference/reference_markers.fasta -out GCF_014635525.1_ASM1463552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:08,084] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:08,087] [INFO] Selected 12 target genomes.
[2024-01-25 20:23:08,087] [INFO] Target genome list was writen to GCF_014635525.1_ASM1463552v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:08,095] [INFO] Task started: fastANI
[2024-01-25 20:23:08,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg2050adf1-9f08-4a4a-be4d-8742f896ed40/GCF_014635525.1_ASM1463552v1_genomic.fna.gz --refList GCF_014635525.1_ASM1463552v1_genomic.fna/target_genomes.txt --output GCF_014635525.1_ASM1463552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:19,485] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:19,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg488ef193-287c-4eac-bd5b-5050fd7ceafa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:19,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg488ef193-287c-4eac-bd5b-5050fd7ceafa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:19,493] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:23:19,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:19,493] [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
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	100.0	1462	1462	95	conclusive
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	99.9999	1460	1462	95	conclusive
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	99.9984	1460	1462	95	conclusive
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	81.5084	822	1462	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	79.7859	678	1462	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	79.3276	668	1462	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	79.0199	625	1462	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	78.9986	611	1462	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	78.5629	528	1462	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	78.5098	481	1462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:19,499] [INFO] DFAST Taxonomy check result was written to GCF_014635525.1_ASM1463552v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:19,500] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:19,500] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:19,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg488ef193-287c-4eac-bd5b-5050fd7ceafa/dqc_reference/checkm_data
[2024-01-25 20:23:19,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:19,558] [INFO] Task started: CheckM
[2024-01-25 20:23:19,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635525.1_ASM1463552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635525.1_ASM1463552v1_genomic.fna/checkm_input GCF_014635525.1_ASM1463552v1_genomic.fna/checkm_result
[2024-01-25 20:24:03,293] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:03,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:03,312] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:03,312] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:03,313] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635525.1_ASM1463552v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:03,313] [INFO] Task started: Blastn
[2024-01-25 20:24:03,313] [INFO] Running command: blastn -query GCF_014635525.1_ASM1463552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg488ef193-287c-4eac-bd5b-5050fd7ceafa/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635525.1_ASM1463552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:04,127] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:04,133] [INFO] Selected 8 target genomes.
[2024-01-25 20:24:04,133] [INFO] Target genome list was writen to GCF_014635525.1_ASM1463552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:04,142] [INFO] Task started: fastANI
[2024-01-25 20:24:04,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg2050adf1-9f08-4a4a-be4d-8742f896ed40/GCF_014635525.1_ASM1463552v1_genomic.fna.gz --refList GCF_014635525.1_ASM1463552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635525.1_ASM1463552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:12,548] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:12,554] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:12,554] [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_004378255.1	s__Mucilaginibacter phyllosphaerae	99.9999	1460	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_003635105.1	s__Mucilaginibacter sp003635105	83.3483	942	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636615.1	s__Mucilaginibacter sp001636615	81.6191	850	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	81.5252	819	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773275.1	s__Mucilaginibacter rigui	81.2601	879	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	80.044	761	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_005938025.2	s__Mucilaginibacter sp005938025	79.709	642	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519315.1	s__Mucilaginibacter psychrotolerans	78.5633	528	1462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:12,555] [INFO] GTDB search result was written to GCF_014635525.1_ASM1463552v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:12,556] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:12,558] [INFO] DFAST_QC result json was written to GCF_014635525.1_ASM1463552v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:12,558] [INFO] DFAST_QC completed!
[2024-01-25 20:24:12,559] [INFO] Total running time: 0h1m22s