[2024-01-25 19:50:05,411] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:05,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:05,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e1d9f60-34f3-4e25-bd36-aee20e0d953a/dqc_reference
[2024-01-25 19:50:06,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:06,568] [INFO] Task started: Prodigal
[2024-01-25 19:50:06,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg846328f9-0468-4c55-b8a8-3d65ea5e75f4/GCF_014773265.1_ASM1477326v1_genomic.fna.gz | prodigal -d GCF_014773265.1_ASM1477326v1_genomic.fna/cds.fna -a GCF_014773265.1_ASM1477326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:30,938] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:30,938] [INFO] Task started: HMMsearch
[2024-01-25 19:50:30,938] [INFO] Running command: hmmsearch --tblout GCF_014773265.1_ASM1477326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e1d9f60-34f3-4e25-bd36-aee20e0d953a/dqc_reference/reference_markers.hmm GCF_014773265.1_ASM1477326v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:31,272] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:31,273] [INFO] Found 6/6 markers.
[2024-01-25 19:50:31,324] [INFO] Query marker FASTA was written to GCF_014773265.1_ASM1477326v1_genomic.fna/markers.fasta
[2024-01-25 19:50:31,324] [INFO] Task started: Blastn
[2024-01-25 19:50:31,324] [INFO] Running command: blastn -query GCF_014773265.1_ASM1477326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e1d9f60-34f3-4e25-bd36-aee20e0d953a/dqc_reference/reference_markers.fasta -out GCF_014773265.1_ASM1477326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:31,896] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:31,899] [INFO] Selected 13 target genomes.
[2024-01-25 19:50:31,899] [INFO] Target genome list was writen to GCF_014773265.1_ASM1477326v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:31,904] [INFO] Task started: fastANI
[2024-01-25 19:50:31,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg846328f9-0468-4c55-b8a8-3d65ea5e75f4/GCF_014773265.1_ASM1477326v1_genomic.fna.gz --refList GCF_014773265.1_ASM1477326v1_genomic.fna/target_genomes.txt --output GCF_014773265.1_ASM1477326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:46,613] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:46,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e1d9f60-34f3-4e25-bd36-aee20e0d953a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:46,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e1d9f60-34f3-4e25-bd36-aee20e0d953a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:46,624] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:50:46,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:46,624] [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 pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	100.0	2104	2106	95	conclusive
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	85.7027	1404	2106	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	81.3668	1135	2106	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	80.3849	1114	2106	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	79.6176	699	2106	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	79.1425	671	2106	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	78.945	630	2106	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	78.3244	543	2106	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	78.1871	418	2106	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	77.5269	338	2106	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	77.521	345	2106	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.1198	298	2106	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	75.9944	69	2106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:46,625] [INFO] DFAST Taxonomy check result was written to GCF_014773265.1_ASM1477326v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:46,626] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:46,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:46,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e1d9f60-34f3-4e25-bd36-aee20e0d953a/dqc_reference/checkm_data
[2024-01-25 19:50:46,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:46,686] [INFO] Task started: CheckM
[2024-01-25 19:50:46,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773265.1_ASM1477326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773265.1_ASM1477326v1_genomic.fna/checkm_input GCF_014773265.1_ASM1477326v1_genomic.fna/checkm_result
[2024-01-25 19:51:49,410] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:49,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:49,454] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:49,454] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:49,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773265.1_ASM1477326v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:49,455] [INFO] Task started: Blastn
[2024-01-25 19:51:49,455] [INFO] Running command: blastn -query GCF_014773265.1_ASM1477326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e1d9f60-34f3-4e25-bd36-aee20e0d953a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773265.1_ASM1477326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:50,326] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:50,334] [INFO] Selected 11 target genomes.
[2024-01-25 19:51:50,334] [INFO] Target genome list was writen to GCF_014773265.1_ASM1477326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:50,361] [INFO] Task started: fastANI
[2024-01-25 19:51:50,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg846328f9-0468-4c55-b8a8-3d65ea5e75f4/GCF_014773265.1_ASM1477326v1_genomic.fna.gz --refList GCF_014773265.1_ASM1477326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014773265.1_ASM1477326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:04,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:04,296] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:04,297] [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_014773265.1	s__Mucilaginibacter pankratovii	100.0	2104	2106	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_004054195.1	s__Mucilaginibacter sp004054195	85.7178	1402	2106	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	81.3717	1134	2106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013915.1	s__Mucilaginibacter pedocola	80.3925	1113	2106	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	79.5957	702	2106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001596135.1	s__Mucilaginibacter sp001596135	79.5328	768	2106	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	79.3791	719	2106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	79.1311	671	2106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	78.5379	633	2106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	77.5176	348	2106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:04,300] [INFO] GTDB search result was written to GCF_014773265.1_ASM1477326v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:04,300] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:04,303] [INFO] DFAST_QC result json was written to GCF_014773265.1_ASM1477326v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:04,303] [INFO] DFAST_QC completed!
[2024-01-25 19:52:04,303] [INFO] Total running time: 0h1m59s