[2024-01-24 14:05:53,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgc345f789-4e49-472e-8af3-f94efff4f61d/dqc_reference
[2024-01-24 14:05:55,087] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,088] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,088] [INFO] Running command: gunzip -c /var/lib/cwl/stga96c7eaa-fec6-40bb-a632-fb08e9d1f4d5/GCF_004378255.1_ASM437825v1_genomic.fna.gz | prodigal -d GCF_004378255.1_ASM437825v1_genomic.fna/cds.fna -a GCF_004378255.1_ASM437825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:14,946] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:14,947] [INFO] Task started: HMMsearch
[2024-01-24 14:06:14,947] [INFO] Running command: hmmsearch --tblout GCF_004378255.1_ASM437825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc345f789-4e49-472e-8af3-f94efff4f61d/dqc_reference/reference_markers.hmm GCF_004378255.1_ASM437825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:15,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:15,307] [INFO] Found 6/6 markers.
[2024-01-24 14:06:15,353] [INFO] Query marker FASTA was written to GCF_004378255.1_ASM437825v1_genomic.fna/markers.fasta
[2024-01-24 14:06:15,354] [INFO] Task started: Blastn
[2024-01-24 14:06:15,354] [INFO] Running command: blastn -query GCF_004378255.1_ASM437825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc345f789-4e49-472e-8af3-f94efff4f61d/dqc_reference/reference_markers.fasta -out GCF_004378255.1_ASM437825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:16,050] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:16,054] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:16,054] [INFO] Target genome list was writen to GCF_004378255.1_ASM437825v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:16,062] [INFO] Task started: fastANI
[2024-01-24 14:06:16,063] [INFO] Running command: fastANI --query /var/lib/cwl/stga96c7eaa-fec6-40bb-a632-fb08e9d1f4d5/GCF_004378255.1_ASM437825v1_genomic.fna.gz --refList GCF_004378255.1_ASM437825v1_genomic.fna/target_genomes.txt --output GCF_004378255.1_ASM437825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:27,985] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:27,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc345f789-4e49-472e-8af3-f94efff4f61d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:27,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc345f789-4e49-472e-8af3-f94efff4f61d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:27,995] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:06:27,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:27,996] [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=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	100.0	1464	1465	95	conclusive
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	99.9968	1455	1465	95	conclusive
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	99.9933	1460	1465	95	conclusive
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	81.4128	832	1465	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	79.9383	666	1465	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	79.3614	665	1465	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	78.9881	629	1465	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	78.9493	615	1465	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	78.5522	482	1465	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	78.545	526	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:27,997] [INFO] DFAST Taxonomy check result was written to GCF_004378255.1_ASM437825v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:27,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:27,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:27,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc345f789-4e49-472e-8af3-f94efff4f61d/dqc_reference/checkm_data
[2024-01-24 14:06:28,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:28,047] [INFO] Task started: CheckM
[2024-01-24 14:06:28,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004378255.1_ASM437825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004378255.1_ASM437825v1_genomic.fna/checkm_input GCF_004378255.1_ASM437825v1_genomic.fna/checkm_result
[2024-01-24 14:07:21,164] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:21,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:21,187] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:21,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:21,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004378255.1_ASM437825v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:21,188] [INFO] Task started: Blastn
[2024-01-24 14:07:21,188] [INFO] Running command: blastn -query GCF_004378255.1_ASM437825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc345f789-4e49-472e-8af3-f94efff4f61d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004378255.1_ASM437825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:22,017] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:22,020] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:22,020] [INFO] Target genome list was writen to GCF_004378255.1_ASM437825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:22,026] [INFO] Task started: fastANI
[2024-01-24 14:07:22,027] [INFO] Running command: fastANI --query /var/lib/cwl/stga96c7eaa-fec6-40bb-a632-fb08e9d1f4d5/GCF_004378255.1_ASM437825v1_genomic.fna.gz --refList GCF_004378255.1_ASM437825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004378255.1_ASM437825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:30,356] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:30,371] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:30,371] [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	100.0	1464	1465	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	83.3273	945	1465	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	81.6771	830	1465	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	81.3818	836	1465	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	81.3032	875	1465	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	80.207	753	1465	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	79.781	644	1465	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	78.545	526	1465	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:30,373] [INFO] GTDB search result was written to GCF_004378255.1_ASM437825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:30,374] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:30,377] [INFO] DFAST_QC result json was written to GCF_004378255.1_ASM437825v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:30,377] [INFO] DFAST_QC completed!
[2024-01-24 14:07:30,377] [INFO] Total running time: 0h1m37s