[2024-01-25 17:48:20,518] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:20,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:20,522] [INFO] DQC Reference Directory: /var/lib/cwl/stgff401d40-a197-4ca5-b3bb-738d0d0a4d45/dqc_reference
[2024-01-25 17:48:21,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:21,740] [INFO] Task started: Prodigal
[2024-01-25 17:48:21,741] [INFO] Running command: gunzip -c /var/lib/cwl/stgd676e1fc-daac-4397-8252-253c21292d8a/GCF_030409405.1_ASM3040940v1_genomic.fna.gz | prodigal -d GCF_030409405.1_ASM3040940v1_genomic.fna/cds.fna -a GCF_030409405.1_ASM3040940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:42,004] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:42,004] [INFO] Task started: HMMsearch
[2024-01-25 17:48:42,004] [INFO] Running command: hmmsearch --tblout GCF_030409405.1_ASM3040940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff401d40-a197-4ca5-b3bb-738d0d0a4d45/dqc_reference/reference_markers.hmm GCF_030409405.1_ASM3040940v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:42,258] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:42,259] [INFO] Found 6/6 markers.
[2024-01-25 17:48:42,298] [INFO] Query marker FASTA was written to GCF_030409405.1_ASM3040940v1_genomic.fna/markers.fasta
[2024-01-25 17:48:42,298] [INFO] Task started: Blastn
[2024-01-25 17:48:42,298] [INFO] Running command: blastn -query GCF_030409405.1_ASM3040940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff401d40-a197-4ca5-b3bb-738d0d0a4d45/dqc_reference/reference_markers.fasta -out GCF_030409405.1_ASM3040940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:42,885] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:42,887] [INFO] Selected 22 target genomes.
[2024-01-25 17:48:42,888] [INFO] Target genome list was writen to GCF_030409405.1_ASM3040940v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:42,908] [INFO] Task started: fastANI
[2024-01-25 17:48:42,908] [INFO] Running command: fastANI --query /var/lib/cwl/stgd676e1fc-daac-4397-8252-253c21292d8a/GCF_030409405.1_ASM3040940v1_genomic.fna.gz --refList GCF_030409405.1_ASM3040940v1_genomic.fna/target_genomes.txt --output GCF_030409405.1_ASM3040940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:06,125] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:06,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff401d40-a197-4ca5-b3bb-738d0d0a4d45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:06,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff401d40-a197-4ca5-b3bb-738d0d0a4d45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:06,137] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:49:06,137] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:06,137] [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 myungsuensis	strain=KCTC 22746	GCA_015222005.1	649104	649104	type	True	99.9992	1682	1685	95	conclusive
Mucilaginibacter mali	strain=G2-14	GCA_013283875.1	2740462	2740462	type	True	78.1336	526	1685	95	below_threshold
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	77.917	372	1685	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	77.671	281	1685	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.6142	202	1685	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.5236	209	1685	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	77.3761	165	1685	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	77.3759	234	1685	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.2631	222	1685	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.2031	274	1685	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.1998	224	1685	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.0559	234	1685	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.0499	235	1685	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.0251	239	1685	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.9662	234	1685	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	76.898	165	1685	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	76.7892	55	1685	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	76.7766	159	1685	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	76.7625	221	1685	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:06,139] [INFO] DFAST Taxonomy check result was written to GCF_030409405.1_ASM3040940v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:06,139] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:06,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:06,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff401d40-a197-4ca5-b3bb-738d0d0a4d45/dqc_reference/checkm_data
[2024-01-25 17:49:06,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:06,189] [INFO] Task started: CheckM
[2024-01-25 17:49:06,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409405.1_ASM3040940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409405.1_ASM3040940v1_genomic.fna/checkm_input GCF_030409405.1_ASM3040940v1_genomic.fna/checkm_result
[2024-01-25 17:50:01,498] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:01,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:01,516] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:01,516] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:01,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409405.1_ASM3040940v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:01,518] [INFO] Task started: Blastn
[2024-01-25 17:50:01,518] [INFO] Running command: blastn -query GCF_030409405.1_ASM3040940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff401d40-a197-4ca5-b3bb-738d0d0a4d45/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409405.1_ASM3040940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:02,394] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:02,397] [INFO] Selected 19 target genomes.
[2024-01-25 17:50:02,397] [INFO] Target genome list was writen to GCF_030409405.1_ASM3040940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:02,417] [INFO] Task started: fastANI
[2024-01-25 17:50:02,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgd676e1fc-daac-4397-8252-253c21292d8a/GCF_030409405.1_ASM3040940v1_genomic.fna.gz --refList GCF_030409405.1_ASM3040940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409405.1_ASM3040940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:21,231] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:21,243] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:21,243] [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_015222005.1	s__Mucilaginibacter myungsuensis	99.9992	1682	1685	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_013283875.1	s__Mucilaginibacter mali	78.1424	524	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221995.1	s__Mucilaginibacter boryungensis	77.926	371	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050755.1	s__Mucilaginibacter yixingensis	77.6748	280	1685	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	77.5812	204	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	77.5236	209	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449775.1	s__Mucilaginibacter sp018449775	77.4846	213	1685	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	77.4731	225	1685	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	77.3431	167	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	77.2752	221	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635105.1	s__Mucilaginibacter sp003635105	77.2334	217	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205845.1	s__Mucilaginibacter sp014205845	77.1913	212	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200495.1	s__Mucilaginibacter sp014200495	77.1712	189	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773265.1	s__Mucilaginibacter pankratovii	77.0674	284	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971525.1	s__Mucilaginibacter ginsenosidivorax	77.0233	241	1685	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	76.9767	233	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	76.9601	240	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	76.8695	168	1685	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013286565.1	s__Mucilaginibacter sp013286565	76.4671	127	1685	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 17:50:21,244] [INFO] GTDB search result was written to GCF_030409405.1_ASM3040940v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:21,245] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:21,250] [INFO] DFAST_QC result json was written to GCF_030409405.1_ASM3040940v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:21,250] [INFO] DFAST_QC completed!
[2024-01-25 17:50:21,250] [INFO] Total running time: 0h2m1s