[2024-01-24 14:19:02,476] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg27693300-a8aa-4836-9e04-e890d95f8b79/dqc_reference
[2024-01-24 14:19:03,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,687] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,688] [INFO] Running command: gunzip -c /var/lib/cwl/stg5105d06e-fdd2-40fc-8f1f-978ec0ceb971/GCF_003351025.1_ASM335102v1_genomic.fna.gz | prodigal -d GCF_003351025.1_ASM335102v1_genomic.fna/cds.fna -a GCF_003351025.1_ASM335102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:35,249] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:35,250] [INFO] Task started: HMMsearch
[2024-01-24 14:19:35,250] [INFO] Running command: hmmsearch --tblout GCF_003351025.1_ASM335102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27693300-a8aa-4836-9e04-e890d95f8b79/dqc_reference/reference_markers.hmm GCF_003351025.1_ASM335102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:35,644] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:35,645] [INFO] Found 6/6 markers.
[2024-01-24 14:19:35,708] [INFO] Query marker FASTA was written to GCF_003351025.1_ASM335102v1_genomic.fna/markers.fasta
[2024-01-24 14:19:35,709] [INFO] Task started: Blastn
[2024-01-24 14:19:35,709] [INFO] Running command: blastn -query GCF_003351025.1_ASM335102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27693300-a8aa-4836-9e04-e890d95f8b79/dqc_reference/reference_markers.fasta -out GCF_003351025.1_ASM335102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:36,336] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:36,340] [INFO] Selected 10 target genomes.
[2024-01-24 14:19:36,340] [INFO] Target genome list was writen to GCF_003351025.1_ASM335102v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:36,344] [INFO] Task started: fastANI
[2024-01-24 14:19:36,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg5105d06e-fdd2-40fc-8f1f-978ec0ceb971/GCF_003351025.1_ASM335102v1_genomic.fna.gz --refList GCF_003351025.1_ASM335102v1_genomic.fna/target_genomes.txt --output GCF_003351025.1_ASM335102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:50,497] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:50,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27693300-a8aa-4836-9e04-e890d95f8b79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:50,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27693300-a8aa-4836-9e04-e890d95f8b79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:50,508] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:50,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:50,509] [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 endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	100.0	2487	2489	95	conclusive
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	94.0121	2068	2489	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	85.7016	1806	2489	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	84.4672	1551	2489	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	84.3178	1555	2489	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.9451	378	2489	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.6584	293	2489	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.6235	301	2489	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.5947	374	2489	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.5934	406	2489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:50,510] [INFO] DFAST Taxonomy check result was written to GCF_003351025.1_ASM335102v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:50,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:50,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:50,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27693300-a8aa-4836-9e04-e890d95f8b79/dqc_reference/checkm_data
[2024-01-24 14:19:50,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:50,581] [INFO] Task started: CheckM
[2024-01-24 14:19:50,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003351025.1_ASM335102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003351025.1_ASM335102v1_genomic.fna/checkm_input GCF_003351025.1_ASM335102v1_genomic.fna/checkm_result
[2024-01-24 14:21:15,110] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:15,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:15,136] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:15,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:15,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003351025.1_ASM335102v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:15,138] [INFO] Task started: Blastn
[2024-01-24 14:21:15,138] [INFO] Running command: blastn -query GCF_003351025.1_ASM335102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27693300-a8aa-4836-9e04-e890d95f8b79/dqc_reference/reference_markers_gtdb.fasta -out GCF_003351025.1_ASM335102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:15,956] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:15,961] [INFO] Selected 7 target genomes.
[2024-01-24 14:21:15,961] [INFO] Target genome list was writen to GCF_003351025.1_ASM335102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:15,982] [INFO] Task started: fastANI
[2024-01-24 14:21:15,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg5105d06e-fdd2-40fc-8f1f-978ec0ceb971/GCF_003351025.1_ASM335102v1_genomic.fna.gz --refList GCF_003351025.1_ASM335102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003351025.1_ASM335102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:29,582] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:29,594] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:29,594] [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_003351025.1	s__Mucilaginibacter endophyticus	100.0	2487	2489	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_003675385.1	s__Mucilaginibacter kameinonensis	94.0101	2069	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.21	95.21	0.87	0.87	2	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	85.7056	1806	2489	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	84.856	1716	2489	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	84.717	1767	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643835.1	s__Mucilaginibacter rubeus	84.4582	1552	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_900100945.1	s__Mucilaginibacter gossypii	84.3131	1556	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:29,596] [INFO] GTDB search result was written to GCF_003351025.1_ASM335102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:29,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:29,599] [INFO] DFAST_QC result json was written to GCF_003351025.1_ASM335102v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:29,600] [INFO] DFAST_QC completed!
[2024-01-24 14:21:29,600] [INFO] Total running time: 0h2m27s