[2024-01-24 12:22:48,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg09908ac8-0a68-4371-9f6b-58ade3776499/dqc_reference
[2024-01-24 12:22:49,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,897] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e4ce310-84fa-4ea7-a5fa-4df60ac2e4f7/GCF_003576455.2_ASM357645v2_genomic.fna.gz | prodigal -d GCF_003576455.2_ASM357645v2_genomic.fna/cds.fna -a GCF_003576455.2_ASM357645v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:21,165] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:21,166] [INFO] Task started: HMMsearch
[2024-01-24 12:23:21,166] [INFO] Running command: hmmsearch --tblout GCF_003576455.2_ASM357645v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09908ac8-0a68-4371-9f6b-58ade3776499/dqc_reference/reference_markers.hmm GCF_003576455.2_ASM357645v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:21,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:21,601] [INFO] Found 6/6 markers.
[2024-01-24 12:23:21,658] [INFO] Query marker FASTA was written to GCF_003576455.2_ASM357645v2_genomic.fna/markers.fasta
[2024-01-24 12:23:21,658] [INFO] Task started: Blastn
[2024-01-24 12:23:21,658] [INFO] Running command: blastn -query GCF_003576455.2_ASM357645v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09908ac8-0a68-4371-9f6b-58ade3776499/dqc_reference/reference_markers.fasta -out GCF_003576455.2_ASM357645v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:22,277] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:22,280] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:22,281] [INFO] Target genome list was writen to GCF_003576455.2_ASM357645v2_genomic.fna/target_genomes.txt
[2024-01-24 12:23:22,285] [INFO] Task started: fastANI
[2024-01-24 12:23:22,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4ce310-84fa-4ea7-a5fa-4df60ac2e4f7/GCF_003576455.2_ASM357645v2_genomic.fna.gz --refList GCF_003576455.2_ASM357645v2_genomic.fna/target_genomes.txt --output GCF_003576455.2_ASM357645v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:39,652] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:39,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09908ac8-0a68-4371-9f6b-58ade3776499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:39,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09908ac8-0a68-4371-9f6b-58ade3776499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:39,666] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:39,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:39,667] [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 celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	100.0	2382	2383	95	conclusive
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	84.2326	1377	2383	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	81.6316	1319	2383	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	81.6146	1345	2383	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	81.579	1241	2383	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	81.4594	1311	2383	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	81.4462	1226	2383	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	78.5139	681	2383	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	78.0075	317	2383	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.828	449	2383	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.7858	429	2383	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.6069	333	2383	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.6051	308	2383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:39,668] [INFO] DFAST Taxonomy check result was written to GCF_003576455.2_ASM357645v2_genomic.fna/tc_result.tsv
[2024-01-24 12:23:39,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:39,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:39,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09908ac8-0a68-4371-9f6b-58ade3776499/dqc_reference/checkm_data
[2024-01-24 12:23:39,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:39,735] [INFO] Task started: CheckM
[2024-01-24 12:23:39,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003576455.2_ASM357645v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003576455.2_ASM357645v2_genomic.fna/checkm_input GCF_003576455.2_ASM357645v2_genomic.fna/checkm_result
[2024-01-24 12:25:02,068] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:02,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:02,095] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:02,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:02,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003576455.2_ASM357645v2_genomic.fna/markers.fasta)
[2024-01-24 12:25:02,096] [INFO] Task started: Blastn
[2024-01-24 12:25:02,096] [INFO] Running command: blastn -query GCF_003576455.2_ASM357645v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09908ac8-0a68-4371-9f6b-58ade3776499/dqc_reference/reference_markers_gtdb.fasta -out GCF_003576455.2_ASM357645v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:02,940] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:02,944] [INFO] Selected 10 target genomes.
[2024-01-24 12:25:02,945] [INFO] Target genome list was writen to GCF_003576455.2_ASM357645v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:02,950] [INFO] Task started: fastANI
[2024-01-24 12:25:02,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4ce310-84fa-4ea7-a5fa-4df60ac2e4f7/GCF_003576455.2_ASM357645v2_genomic.fna.gz --refList GCF_003576455.2_ASM357645v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003576455.2_ASM357645v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:19,669] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:19,683] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:19,683] [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_003576455.2	s__Mucilaginibacter celer	100.0	2381	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148845.1	s__Mucilaginibacter oryzae	84.2515	1375	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675385.1	s__Mucilaginibacter kameinonensis	81.6424	1317	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.21	95.21	0.87	0.87	2	-
GCF_003351025.1	s__Mucilaginibacter endophyticus	81.606	1348	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664165.1	s__Mucilaginibacter sp003664165	81.6001	1367	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643835.1	s__Mucilaginibacter rubeus	81.5795	1240	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	81.4706	1309	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100945.1	s__Mucilaginibacter gossypii	81.4648	1222	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
GCF_003208075.1	s__Mucilaginibacter sp003208075	81.4188	1302	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089895.1	s__Mucilaginibacter inviolabilis	78.5113	682	2383	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 12:25:19,685] [INFO] GTDB search result was written to GCF_003576455.2_ASM357645v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:19,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:19,689] [INFO] DFAST_QC result json was written to GCF_003576455.2_ASM357645v2_genomic.fna/dqc_result.json
[2024-01-24 12:25:19,689] [INFO] DFAST_QC completed!
[2024-01-24 12:25:19,689] [INFO] Total running time: 0h2m31s