[2024-01-24 12:52:23,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:23,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:23,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg9df02fcd-20cd-4b00-b2f2-5e833f15f287/dqc_reference
[2024-01-24 12:52:24,432] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:24,432] [INFO] Task started: Prodigal
[2024-01-24 12:52:24,433] [INFO] Running command: gunzip -c /var/lib/cwl/stga62f5dd1-9012-45fc-9ac0-60d9c6582105/GCF_024498135.1_ASM2449813v1_genomic.fna.gz | prodigal -d GCF_024498135.1_ASM2449813v1_genomic.fna/cds.fna -a GCF_024498135.1_ASM2449813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:49,686] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:49,687] [INFO] Task started: HMMsearch
[2024-01-24 12:52:49,687] [INFO] Running command: hmmsearch --tblout GCF_024498135.1_ASM2449813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9df02fcd-20cd-4b00-b2f2-5e833f15f287/dqc_reference/reference_markers.hmm GCF_024498135.1_ASM2449813v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:50,030] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:50,032] [INFO] Found 6/6 markers.
[2024-01-24 12:52:50,080] [INFO] Query marker FASTA was written to GCF_024498135.1_ASM2449813v1_genomic.fna/markers.fasta
[2024-01-24 12:52:50,080] [INFO] Task started: Blastn
[2024-01-24 12:52:50,080] [INFO] Running command: blastn -query GCF_024498135.1_ASM2449813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9df02fcd-20cd-4b00-b2f2-5e833f15f287/dqc_reference/reference_markers.fasta -out GCF_024498135.1_ASM2449813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:50,704] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:50,708] [INFO] Selected 10 target genomes.
[2024-01-24 12:52:50,709] [INFO] Target genome list was writen to GCF_024498135.1_ASM2449813v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:50,725] [INFO] Task started: fastANI
[2024-01-24 12:52:50,725] [INFO] Running command: fastANI --query /var/lib/cwl/stga62f5dd1-9012-45fc-9ac0-60d9c6582105/GCF_024498135.1_ASM2449813v1_genomic.fna.gz --refList GCF_024498135.1_ASM2449813v1_genomic.fna/target_genomes.txt --output GCF_024498135.1_ASM2449813v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:00,398] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:00,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9df02fcd-20cd-4b00-b2f2-5e833f15f287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:00,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9df02fcd-20cd-4b00-b2f2-5e833f15f287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:00,408] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:53:00,408] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:53:00,408] [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 terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	82.1265	975	1976	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	81.185	839	1976	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	81.1477	844	1976	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	81.1327	846	1976	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	79.2172	700	1976	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	79.1917	616	1976	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	78.9772	654	1976	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	78.9472	649	1976	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	78.5437	510	1976	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.4355	262	1976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:00,413] [INFO] DFAST Taxonomy check result was written to GCF_024498135.1_ASM2449813v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:00,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:00,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:00,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9df02fcd-20cd-4b00-b2f2-5e833f15f287/dqc_reference/checkm_data
[2024-01-24 12:53:00,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:00,476] [INFO] Task started: CheckM
[2024-01-24 12:53:00,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498135.1_ASM2449813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498135.1_ASM2449813v1_genomic.fna/checkm_input GCF_024498135.1_ASM2449813v1_genomic.fna/checkm_result
[2024-01-24 12:54:07,219] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:07,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:07,244] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:07,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:07,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498135.1_ASM2449813v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:07,245] [INFO] Task started: Blastn
[2024-01-24 12:54:07,245] [INFO] Running command: blastn -query GCF_024498135.1_ASM2449813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9df02fcd-20cd-4b00-b2f2-5e833f15f287/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498135.1_ASM2449813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:08,042] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:08,047] [INFO] Selected 9 target genomes.
[2024-01-24 12:54:08,048] [INFO] Target genome list was writen to GCF_024498135.1_ASM2449813v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:08,077] [INFO] Task started: fastANI
[2024-01-24 12:54:08,077] [INFO] Running command: fastANI --query /var/lib/cwl/stga62f5dd1-9012-45fc-9ac0-60d9c6582105/GCF_024498135.1_ASM2449813v1_genomic.fna.gz --refList GCF_024498135.1_ASM2449813v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498135.1_ASM2449813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:17,227] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:17,242] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:54:17,243] [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_001636615.1	s__Mucilaginibacter sp001636615	82.1923	995	1976	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	82.1269	976	1976	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773275.1	s__Mucilaginibacter rigui	82.0092	970	1976	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	81.6493	890	1976	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	81.1623	843	1976	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	80.674	890	1976	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_005938025.2	s__Mucilaginibacter sp005938025	79.7668	700	1976	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773245.1	s__Mucilaginibacter glaciei	79.1954	615	1976	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	79.0128	648	1976	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 12:54:17,244] [INFO] GTDB search result was written to GCF_024498135.1_ASM2449813v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:17,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:17,248] [INFO] DFAST_QC result json was written to GCF_024498135.1_ASM2449813v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:17,248] [INFO] DFAST_QC completed!
[2024-01-24 12:54:17,249] [INFO] Total running time: 0h1m54s