[2024-01-24 11:12:25,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:25,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:25,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgfae31d6e-c040-402a-967b-a74b1fa23dbb/dqc_reference
[2024-01-24 11:12:27,191] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,192] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,192] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaf71ada-71d8-42a4-ae55-323c88330094/GCF_013087555.1_ASM1308755v1_genomic.fna.gz | prodigal -d GCF_013087555.1_ASM1308755v1_genomic.fna/cds.fna -a GCF_013087555.1_ASM1308755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:36,955] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:36,956] [INFO] Task started: HMMsearch
[2024-01-24 11:12:36,956] [INFO] Running command: hmmsearch --tblout GCF_013087555.1_ASM1308755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfae31d6e-c040-402a-967b-a74b1fa23dbb/dqc_reference/reference_markers.hmm GCF_013087555.1_ASM1308755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:37,237] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:37,238] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaaf71ada-71d8-42a4-ae55-323c88330094/GCF_013087555.1_ASM1308755v1_genomic.fna.gz]
[2024-01-24 11:12:37,273] [INFO] Query marker FASTA was written to GCF_013087555.1_ASM1308755v1_genomic.fna/markers.fasta
[2024-01-24 11:12:37,274] [INFO] Task started: Blastn
[2024-01-24 11:12:37,274] [INFO] Running command: blastn -query GCF_013087555.1_ASM1308755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfae31d6e-c040-402a-967b-a74b1fa23dbb/dqc_reference/reference_markers.fasta -out GCF_013087555.1_ASM1308755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:37,806] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:37,809] [INFO] Selected 12 target genomes.
[2024-01-24 11:12:37,809] [INFO] Target genome list was writen to GCF_013087555.1_ASM1308755v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:37,825] [INFO] Task started: fastANI
[2024-01-24 11:12:37,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaf71ada-71d8-42a4-ae55-323c88330094/GCF_013087555.1_ASM1308755v1_genomic.fna.gz --refList GCF_013087555.1_ASM1308755v1_genomic.fna/target_genomes.txt --output GCF_013087555.1_ASM1308755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:48,629] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:48,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfae31d6e-c040-402a-967b-a74b1fa23dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:48,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfae31d6e-c040-402a-967b-a74b1fa23dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:48,650] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:48,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:48,651] [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 humi	strain=S1162	GCA_013087555.1	2732510	2732510	type	True	100.0	781	784	95	conclusive
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	80.1771	371	784	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	78.1996	137	784	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	78.0945	175	784	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	78.0245	175	784	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.9358	167	784	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.7854	184	784	95	below_threshold
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	77.6999	136	784	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	77.5202	170	784	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.504	164	784	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	77.4859	154	784	95	below_threshold
Mucilaginibacter segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	77.3403	126	784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:48,667] [INFO] DFAST Taxonomy check result was written to GCF_013087555.1_ASM1308755v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:48,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:48,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:48,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfae31d6e-c040-402a-967b-a74b1fa23dbb/dqc_reference/checkm_data
[2024-01-24 11:12:48,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:48,718] [INFO] Task started: CheckM
[2024-01-24 11:12:48,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013087555.1_ASM1308755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013087555.1_ASM1308755v1_genomic.fna/checkm_input GCF_013087555.1_ASM1308755v1_genomic.fna/checkm_result
[2024-01-24 11:13:20,605] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:20,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,631] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:20,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:20,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013087555.1_ASM1308755v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:20,632] [INFO] Task started: Blastn
[2024-01-24 11:13:20,632] [INFO] Running command: blastn -query GCF_013087555.1_ASM1308755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfae31d6e-c040-402a-967b-a74b1fa23dbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013087555.1_ASM1308755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:21,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:21,110] [INFO] Selected 11 target genomes.
[2024-01-24 11:13:21,111] [INFO] Target genome list was writen to GCF_013087555.1_ASM1308755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:21,120] [INFO] Task started: fastANI
[2024-01-24 11:13:21,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaf71ada-71d8-42a4-ae55-323c88330094/GCF_013087555.1_ASM1308755v1_genomic.fna.gz --refList GCF_013087555.1_ASM1308755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013087555.1_ASM1308755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:30,476] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:30,488] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:13:30,488] [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
GCA_014376655.1	s__Mucilaginibacter sp014376655	83.6917	335	784	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	80.3995	350	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCF_007558865.1	s__Mucilaginibacter corticis	80.1617	372	784	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	79.3598	322	784	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	78.321	172	784	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	77.9557	172	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.00	99.00	0.77	0.77	2	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	77.7278	156	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	77.6942	171	784	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	77.4874	164	784	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	77.466	155	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110415.1	s__Mucilaginibacter sp900110415	77.352	200	784	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 11:13:30,491] [INFO] GTDB search result was written to GCF_013087555.1_ASM1308755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:30,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:30,495] [INFO] DFAST_QC result json was written to GCF_013087555.1_ASM1308755v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:30,495] [INFO] DFAST_QC completed!
[2024-01-24 11:13:30,495] [INFO] Total running time: 0h1m5s