[2024-01-24 12:30:48,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:48,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:48,113] [INFO] DQC Reference Directory: /var/lib/cwl/stgce854597-53fd-4253-9962-c45443fdd842/dqc_reference
[2024-01-24 12:30:49,230] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:49,230] [INFO] Task started: Prodigal
[2024-01-24 12:30:49,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg29757d68-f421-41b4-9581-3cccadfdaf1b/GCF_007558865.1_ASM755886v1_genomic.fna.gz | prodigal -d GCF_007558865.1_ASM755886v1_genomic.fna/cds.fna -a GCF_007558865.1_ASM755886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:07,900] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:07,901] [INFO] Task started: HMMsearch
[2024-01-24 12:31:07,901] [INFO] Running command: hmmsearch --tblout GCF_007558865.1_ASM755886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce854597-53fd-4253-9962-c45443fdd842/dqc_reference/reference_markers.hmm GCF_007558865.1_ASM755886v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:08,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:08,192] [INFO] Found 6/6 markers.
[2024-01-24 12:31:08,235] [INFO] Query marker FASTA was written to GCF_007558865.1_ASM755886v1_genomic.fna/markers.fasta
[2024-01-24 12:31:08,235] [INFO] Task started: Blastn
[2024-01-24 12:31:08,235] [INFO] Running command: blastn -query GCF_007558865.1_ASM755886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce854597-53fd-4253-9962-c45443fdd842/dqc_reference/reference_markers.fasta -out GCF_007558865.1_ASM755886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:08,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:08,820] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:08,821] [INFO] Target genome list was writen to GCF_007558865.1_ASM755886v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:08,827] [INFO] Task started: fastANI
[2024-01-24 12:31:08,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg29757d68-f421-41b4-9581-3cccadfdaf1b/GCF_007558865.1_ASM755886v1_genomic.fna.gz --refList GCF_007558865.1_ASM755886v1_genomic.fna/target_genomes.txt --output GCF_007558865.1_ASM755886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:28,509] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:28,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce854597-53fd-4253-9962-c45443fdd842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:28,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce854597-53fd-4253-9962-c45443fdd842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:28,522] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:28,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:28,522] [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 corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	100.0	1773	1773	95	conclusive
Mucilaginibacter humi	strain=S1162	GCA_013087555.1	2732510	2732510	type	True	80.1794	374	1773	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	78.386	294	1773	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.9975	371	1773	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.9935	319	1773	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.9345	406	1773	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	77.9007	353	1773	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.882	327	1773	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	77.8586	360	1773	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	77.8341	355	1773	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.7517	238	1773	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	77.7012	292	1773	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.6186	246	1773	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.5993	244	1773	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.5973	314	1773	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.5889	282	1773	95	below_threshold
Mucilaginibacter hurinus	strain=ZR32	GCA_003324525.1	2201324	2201324	type	True	77.586	185	1773	95	below_threshold
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	77.5796	335	1773	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	77.5402	292	1773	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	77.5073	284	1773	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	77.4891	190	1773	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	77.3264	280	1773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:28,523] [INFO] DFAST Taxonomy check result was written to GCF_007558865.1_ASM755886v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:28,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:28,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:28,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce854597-53fd-4253-9962-c45443fdd842/dqc_reference/checkm_data
[2024-01-24 12:31:28,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:28,574] [INFO] Task started: CheckM
[2024-01-24 12:31:28,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007558865.1_ASM755886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007558865.1_ASM755886v1_genomic.fna/checkm_input GCF_007558865.1_ASM755886v1_genomic.fna/checkm_result
[2024-01-24 12:32:19,642] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:19,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:19,658] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:19,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:19,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007558865.1_ASM755886v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:19,659] [INFO] Task started: Blastn
[2024-01-24 12:32:19,659] [INFO] Running command: blastn -query GCF_007558865.1_ASM755886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce854597-53fd-4253-9962-c45443fdd842/dqc_reference/reference_markers_gtdb.fasta -out GCF_007558865.1_ASM755886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:20,421] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:20,424] [INFO] Selected 15 target genomes.
[2024-01-24 12:32:20,424] [INFO] Target genome list was writen to GCF_007558865.1_ASM755886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:20,431] [INFO] Task started: fastANI
[2024-01-24 12:32:20,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg29757d68-f421-41b4-9581-3cccadfdaf1b/GCF_007558865.1_ASM755886v1_genomic.fna.gz --refList GCF_007558865.1_ASM755886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007558865.1_ASM755886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:32,803] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:32,812] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:32,812] [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_007558865.1	s__Mucilaginibacter corticis	100.0	1772	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014376655.1	s__Mucilaginibacter sp014376655	80.2701	451	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403905.1	s__Mucilaginibacter sp002403905	80.2579	619	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCF_018449775.1	s__Mucilaginibacter sp018449775	79.2373	718	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288485.1	s__Mucilaginibacter sp013288485	78.7722	323	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885865.1	s__Mucilaginibacter sp903885865	78.3112	341	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.00	99.00	0.77	0.77	2	-
GCA_013288465.1	s__Mucilaginibacter sp013288465	78.1778	186	1773	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	77.9689	322	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938025.2	s__Mucilaginibacter sp005938025	77.9682	319	1773	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	77.8717	328	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900110415.1	s__Mucilaginibacter sp900110415	77.8179	345	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324525.1	s__Mucilaginibacter hurinus	77.586	185	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432115.1	s__Mucilaginibacter sp003432115	77.5786	316	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001911425.1	s__Mucilaginibacter polytrichastri	77.5073	284	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003432065.1	s__Mucilaginibacter sp003432065	77.4891	190	1773	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 12:32:32,813] [INFO] GTDB search result was written to GCF_007558865.1_ASM755886v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:32,814] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:32,817] [INFO] DFAST_QC result json was written to GCF_007558865.1_ASM755886v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:32,817] [INFO] DFAST_QC completed!
[2024-01-24 12:32:32,817] [INFO] Total running time: 0h1m45s