[2024-01-25 20:21:20,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:20,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:20,505] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0e79508-1013-4c01-84ff-bdb3cd53050c/dqc_reference
[2024-01-25 20:21:21,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:21,639] [INFO] Task started: Prodigal
[2024-01-25 20:21:21,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgf73a413c-e141-46fa-8385-153f984be7e9/GCF_030409325.1_ASM3040932v1_genomic.fna.gz | prodigal -d GCF_030409325.1_ASM3040932v1_genomic.fna/cds.fna -a GCF_030409325.1_ASM3040932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:42,650] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:42,651] [INFO] Task started: HMMsearch
[2024-01-25 20:21:42,651] [INFO] Running command: hmmsearch --tblout GCF_030409325.1_ASM3040932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0e79508-1013-4c01-84ff-bdb3cd53050c/dqc_reference/reference_markers.hmm GCF_030409325.1_ASM3040932v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:42,973] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:42,975] [INFO] Found 6/6 markers.
[2024-01-25 20:21:43,023] [INFO] Query marker FASTA was written to GCF_030409325.1_ASM3040932v1_genomic.fna/markers.fasta
[2024-01-25 20:21:43,023] [INFO] Task started: Blastn
[2024-01-25 20:21:43,023] [INFO] Running command: blastn -query GCF_030409325.1_ASM3040932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e79508-1013-4c01-84ff-bdb3cd53050c/dqc_reference/reference_markers.fasta -out GCF_030409325.1_ASM3040932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:43,601] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:43,604] [INFO] Selected 15 target genomes.
[2024-01-25 20:21:43,604] [INFO] Target genome list was writen to GCF_030409325.1_ASM3040932v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:43,610] [INFO] Task started: fastANI
[2024-01-25 20:21:43,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgf73a413c-e141-46fa-8385-153f984be7e9/GCF_030409325.1_ASM3040932v1_genomic.fna.gz --refList GCF_030409325.1_ASM3040932v1_genomic.fna/target_genomes.txt --output GCF_030409325.1_ASM3040932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:01,089] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:01,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0e79508-1013-4c01-84ff-bdb3cd53050c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:01,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0e79508-1013-4c01-84ff-bdb3cd53050c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:01,100] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:22:01,100] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:22:01,100] [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 lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	80.6438	933	2040	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	80.638	934	2040	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	80.6096	930	2040	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	79.5916	758	2040	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	78.9964	714	2040	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	78.8503	695	2040	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	78.7695	697	2040	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	78.7048	683	2040	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	78.5774	681	2040	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	78.1357	402	2040	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	78.0038	316	2040	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.8589	261	2040	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.8082	349	2040	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.6643	376	2040	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.6227	287	2040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:01,101] [INFO] DFAST Taxonomy check result was written to GCF_030409325.1_ASM3040932v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:01,103] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:01,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:01,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0e79508-1013-4c01-84ff-bdb3cd53050c/dqc_reference/checkm_data
[2024-01-25 20:22:01,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:01,162] [INFO] Task started: CheckM
[2024-01-25 20:22:01,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409325.1_ASM3040932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409325.1_ASM3040932v1_genomic.fna/checkm_input GCF_030409325.1_ASM3040932v1_genomic.fna/checkm_result
[2024-01-25 20:22:59,382] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:59,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:59,401] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:59,401] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:59,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409325.1_ASM3040932v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:59,402] [INFO] Task started: Blastn
[2024-01-25 20:22:59,402] [INFO] Running command: blastn -query GCF_030409325.1_ASM3040932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e79508-1013-4c01-84ff-bdb3cd53050c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409325.1_ASM3040932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:00,214] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:00,218] [INFO] Selected 12 target genomes.
[2024-01-25 20:23:00,218] [INFO] Target genome list was writen to GCF_030409325.1_ASM3040932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:00,236] [INFO] Task started: fastANI
[2024-01-25 20:23:00,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgf73a413c-e141-46fa-8385-153f984be7e9/GCF_030409325.1_ASM3040932v1_genomic.fna.gz --refList GCF_030409325.1_ASM3040932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409325.1_ASM3040932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:17,744] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:17,753] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:23:17,753] [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_014200575.1	s__Mucilaginibacter sp014200575	80.93	949	2040	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	80.7488	986	2040	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	80.6386	933	2040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	-
GCF_011089895.1	s__Mucilaginibacter inviolabilis	80.606	932	2040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149275.1	s__Mucilaginibacter sp013149275	80.5802	940	2040	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	79.5591	763	2040	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	79.2633	741	2040	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	79.1159	696	2040	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	78.9897	715	2040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664165.1	s__Mucilaginibacter sp003664165	78.7163	713	2040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208075.1	s__Mucilaginibacter sp003208075	78.66	707	2040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105165.1	s__Mucilaginibacter mallensis	78.1214	403	2040	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 20:23:17,760] [INFO] GTDB search result was written to GCF_030409325.1_ASM3040932v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:17,761] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:17,764] [INFO] DFAST_QC result json was written to GCF_030409325.1_ASM3040932v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:17,764] [INFO] DFAST_QC completed!
[2024-01-25 20:23:17,764] [INFO] Total running time: 0h1m57s