[2024-01-24 13:41:10,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,393] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,393] [INFO] DQC Reference Directory: /var/lib/cwl/stgab17d3ba-8ce4-47b7-b536-1d2727aca2a2/dqc_reference
[2024-01-24 13:41:11,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,698] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,698] [INFO] Running command: gunzip -c /var/lib/cwl/stgad2e47f8-0d0c-4dc4-8741-1f66806b9ed3/GCF_003584165.1_ASM358416v1_genomic.fna.gz | prodigal -d GCF_003584165.1_ASM358416v1_genomic.fna/cds.fna -a GCF_003584165.1_ASM358416v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:39,687] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:39,688] [INFO] Task started: HMMsearch
[2024-01-24 13:41:39,688] [INFO] Running command: hmmsearch --tblout GCF_003584165.1_ASM358416v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab17d3ba-8ce4-47b7-b536-1d2727aca2a2/dqc_reference/reference_markers.hmm GCF_003584165.1_ASM358416v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:39,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:39,967] [INFO] Found 6/6 markers.
[2024-01-24 13:41:40,004] [INFO] Query marker FASTA was written to GCF_003584165.1_ASM358416v1_genomic.fna/markers.fasta
[2024-01-24 13:41:40,005] [INFO] Task started: Blastn
[2024-01-24 13:41:40,005] [INFO] Running command: blastn -query GCF_003584165.1_ASM358416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab17d3ba-8ce4-47b7-b536-1d2727aca2a2/dqc_reference/reference_markers.fasta -out GCF_003584165.1_ASM358416v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:40,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:40,671] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:40,672] [INFO] Target genome list was writen to GCF_003584165.1_ASM358416v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:40,675] [INFO] Task started: fastANI
[2024-01-24 13:41:40,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgad2e47f8-0d0c-4dc4-8741-1f66806b9ed3/GCF_003584165.1_ASM358416v1_genomic.fna.gz --refList GCF_003584165.1_ASM358416v1_genomic.fna/target_genomes.txt --output GCF_003584165.1_ASM358416v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:49,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:49,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab17d3ba-8ce4-47b7-b536-1d2727aca2a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:49,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab17d3ba-8ce4-47b7-b536-1d2727aca2a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:49,802] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:49,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:49,803] [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
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	100.0	1395	1398	95	conclusive
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	100.0	1395	1398	95	conclusive
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	94.229	1120	1398	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	94.2275	1120	1398	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	86.7397	1022	1398	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	81.0905	668	1398	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	80.7372	686	1398	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	79.4618	543	1398	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	77.5409	260	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,804] [INFO] DFAST Taxonomy check result was written to GCF_003584165.1_ASM358416v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:49,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:49,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:49,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab17d3ba-8ce4-47b7-b536-1d2727aca2a2/dqc_reference/checkm_data
[2024-01-24 13:41:49,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:49,844] [INFO] Task started: CheckM
[2024-01-24 13:41:49,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003584165.1_ASM358416v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003584165.1_ASM358416v1_genomic.fna/checkm_input GCF_003584165.1_ASM358416v1_genomic.fna/checkm_result
[2024-01-24 13:42:59,242] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:59,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:59,260] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:59,260] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:59,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003584165.1_ASM358416v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:59,260] [INFO] Task started: Blastn
[2024-01-24 13:42:59,261] [INFO] Running command: blastn -query GCF_003584165.1_ASM358416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab17d3ba-8ce4-47b7-b536-1d2727aca2a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003584165.1_ASM358416v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:00,055] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:00,058] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:00,058] [INFO] Target genome list was writen to GCF_003584165.1_ASM358416v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:00,080] [INFO] Task started: fastANI
[2024-01-24 13:43:00,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgad2e47f8-0d0c-4dc4-8741-1f66806b9ed3/GCF_003584165.1_ASM358416v1_genomic.fna.gz --refList GCF_003584165.1_ASM358416v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003584165.1_ASM358416v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:08,883] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:08,893] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:08,893] [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_003584165.1	s__Muricauda sp003584165	100.0	1395	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003584135.1	s__Muricauda sp003584135	94.2232	1119	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010500845.1	s__Muricauda sediminis	86.7365	1022	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	81.37	667	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_003058265.1	s__Muricauda sp003058265	81.1001	667	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	80.7272	686	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	80.287	677	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	79.1857	517	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_009184425.1	s__Muricauda olearia	78.9792	515	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_010468565.1	s__Muricauda sp010468565	78.9781	531	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	78.6019	532	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:08,895] [INFO] GTDB search result was written to GCF_003584165.1_ASM358416v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:08,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:08,898] [INFO] DFAST_QC result json was written to GCF_003584165.1_ASM358416v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:08,898] [INFO] DFAST_QC completed!
[2024-01-24 13:43:08,898] [INFO] Total running time: 0h1m59s