[2024-01-25 19:49:20,650] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c39b878-c4b9-4bcf-bc09-4d89b3f59dc1/dqc_reference
[2024-01-25 19:49:21,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:21,772] [INFO] Task started: Prodigal
[2024-01-25 19:49:21,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg602dbaa5-a95e-4602-b5e8-eb9d61e5bc78/GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/cds.fna -a GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:41,621] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:41,622] [INFO] Task started: HMMsearch
[2024-01-25 19:49:41,622] [INFO] Running command: hmmsearch --tblout GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c39b878-c4b9-4bcf-bc09-4d89b3f59dc1/dqc_reference/reference_markers.hmm GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:41,908] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:41,910] [INFO] Found 6/6 markers.
[2024-01-25 19:49:41,953] [INFO] Query marker FASTA was written to GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:49:41,954] [INFO] Task started: Blastn
[2024-01-25 19:49:41,954] [INFO] Running command: blastn -query GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c39b878-c4b9-4bcf-bc09-4d89b3f59dc1/dqc_reference/reference_markers.fasta -out GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:42,532] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:42,535] [INFO] Selected 16 target genomes.
[2024-01-25 19:49:42,536] [INFO] Target genome list was writen to GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:49:42,555] [INFO] Task started: fastANI
[2024-01-25 19:49:42,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg602dbaa5-a95e-4602-b5e8-eb9d61e5bc78/GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna.gz --refList GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:58,097] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:58,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c39b878-c4b9-4bcf-bc09-4d89b3f59dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:58,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c39b878-c4b9-4bcf-bc09-4d89b3f59dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:58,108] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:49:58,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:58,109] [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 polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	100.0	1916	1922	95	conclusive
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	99.9911	1916	1922	95	conclusive
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	80.479	859	1922	95	below_threshold
Mucilaginibacter aquatilis	strain=HME9299	GCA_009755275.1	1517760	1517760	type	True	77.7962	217	1922	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.607	363	1922	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	77.5508	316	1922	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.5241	228	1922	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.4503	318	1922	95	below_threshold
Mucilaginibacter ginkgonis	strain=HMF7856	GCA_009754905.2	2682091	2682091	type	True	77.4252	265	1922	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.3091	319	1922	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.295	311	1922	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.2413	292	1922	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	77.2326	240	1922	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.113	248	1922	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.0902	313	1922	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	76.596	195	1922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:58,110] [INFO] DFAST Taxonomy check result was written to GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:49:58,111] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:58,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:58,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c39b878-c4b9-4bcf-bc09-4d89b3f59dc1/dqc_reference/checkm_data
[2024-01-25 19:49:58,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:58,166] [INFO] Task started: CheckM
[2024-01-25 19:49:58,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/checkm_input GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:50:52,784] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:52,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:52,802] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:52,802] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:52,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:50:52,803] [INFO] Task started: Blastn
[2024-01-25 19:50:52,803] [INFO] Running command: blastn -query GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c39b878-c4b9-4bcf-bc09-4d89b3f59dc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:53,641] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:53,644] [INFO] Selected 16 target genomes.
[2024-01-25 19:50:53,644] [INFO] Target genome list was writen to GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:53,666] [INFO] Task started: fastANI
[2024-01-25 19:50:53,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg602dbaa5-a95e-4602-b5e8-eb9d61e5bc78/GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna.gz --refList GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:09,528] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:09,539] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:09,539] [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_001911425.1	s__Mucilaginibacter polytrichastri	99.9911	1916	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_903644075.1	s__Mucilaginibacter sp903644075	82.7612	912	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928685.1	s__Mucilaginibacter sp009928685	80.4758	859	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755275.1	s__Mucilaginibacter aquatilis	77.7962	217	1922	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	77.5998	330	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101875.1	s__Mucilaginibacter pineti	77.5983	364	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635825.1	s__Mucilaginibacter galii	77.5604	315	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	77.4822	328	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009754905.2	s__Mucilaginibacter ginkgonis	77.4139	266	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009770985.1	s__Mucilaginibacter sp009770985	77.3175	264	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773245.1	s__Mucilaginibacter glaciei	77.2958	310	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007558865.1	s__Mucilaginibacter corticis	77.2413	292	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376655.1	s__Mucilaginibacter sp014376655	77.2325	161	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155965.1	s__Mucilaginibacter lappiensis	77.1421	336	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	-
GCA_903885865.1	s__Mucilaginibacter sp903885865	76.6184	131	1922	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.00	99.00	0.77	0.77	2	-
GCF_003432065.1	s__Mucilaginibacter sp003432065	76.596	195	1922	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 19:51:09,540] [INFO] GTDB search result was written to GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:09,541] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:09,544] [INFO] DFAST_QC result json was written to GCF_900116355.1_IMG-taxon_2622736518_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:51:09,544] [INFO] DFAST_QC completed!
[2024-01-25 19:51:09,544] [INFO] Total running time: 0h1m49s