[2024-01-24 11:43:53,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg848d8b40-3ecf-4cf0-b1f4-3f879542b290/dqc_reference
[2024-01-24 11:43:54,327] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,328] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,328] [INFO] Running command: gunzip -c /var/lib/cwl/stg44071e9b-5b74-4bb3-9e4e-d3eeedcdb833/GCF_003173595.1_ASM317359v1_genomic.fna.gz | prodigal -d GCF_003173595.1_ASM317359v1_genomic.fna/cds.fna -a GCF_003173595.1_ASM317359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:11,435] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:11,435] [INFO] Task started: HMMsearch
[2024-01-24 11:44:11,435] [INFO] Running command: hmmsearch --tblout GCF_003173595.1_ASM317359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg848d8b40-3ecf-4cf0-b1f4-3f879542b290/dqc_reference/reference_markers.hmm GCF_003173595.1_ASM317359v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:11,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:11,703] [INFO] Found 6/6 markers.
[2024-01-24 11:44:11,741] [INFO] Query marker FASTA was written to GCF_003173595.1_ASM317359v1_genomic.fna/markers.fasta
[2024-01-24 11:44:11,741] [INFO] Task started: Blastn
[2024-01-24 11:44:11,742] [INFO] Running command: blastn -query GCF_003173595.1_ASM317359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg848d8b40-3ecf-4cf0-b1f4-3f879542b290/dqc_reference/reference_markers.fasta -out GCF_003173595.1_ASM317359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:12,352] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:12,359] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:12,359] [INFO] Target genome list was writen to GCF_003173595.1_ASM317359v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:12,366] [INFO] Task started: fastANI
[2024-01-24 11:44:12,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg44071e9b-5b74-4bb3-9e4e-d3eeedcdb833/GCF_003173595.1_ASM317359v1_genomic.fna.gz --refList GCF_003173595.1_ASM317359v1_genomic.fna/target_genomes.txt --output GCF_003173595.1_ASM317359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:28,480] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:28,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg848d8b40-3ecf-4cf0-b1f4-3f879542b290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:28,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg848d8b40-3ecf-4cf0-b1f4-3f879542b290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:28,494] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:28,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:28,494] [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
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	100.0	1452	1453	95	conclusive
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	82.4992	949	1453	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	80.4639	637	1453	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.1774	604	1453	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	80.1421	617	1453	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	80.0866	613	1453	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	80.0762	597	1453	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	80.0327	638	1453	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	79.9695	561	1453	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	79.9091	600	1453	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	79.8501	605	1453	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.7629	582	1453	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	79.6274	578	1453	95	below_threshold
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	79.4792	539	1453	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	79.4299	534	1453	95	below_threshold
Pedobacter changchengzhani	strain=E01020	GCA_004354365.1	2529274	2529274	type	True	78.9306	399	1453	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:28,496] [INFO] DFAST Taxonomy check result was written to GCF_003173595.1_ASM317359v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:28,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:28,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:28,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg848d8b40-3ecf-4cf0-b1f4-3f879542b290/dqc_reference/checkm_data
[2024-01-24 11:44:28,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:28,540] [INFO] Task started: CheckM
[2024-01-24 11:44:28,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003173595.1_ASM317359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003173595.1_ASM317359v1_genomic.fna/checkm_input GCF_003173595.1_ASM317359v1_genomic.fna/checkm_result
[2024-01-24 11:45:17,121] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:17,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,140] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:17,140] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:17,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003173595.1_ASM317359v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:17,141] [INFO] Task started: Blastn
[2024-01-24 11:45:17,141] [INFO] Running command: blastn -query GCF_003173595.1_ASM317359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg848d8b40-3ecf-4cf0-b1f4-3f879542b290/dqc_reference/reference_markers_gtdb.fasta -out GCF_003173595.1_ASM317359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:17,939] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:17,942] [INFO] Selected 13 target genomes.
[2024-01-24 11:45:17,943] [INFO] Target genome list was writen to GCF_003173595.1_ASM317359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:17,951] [INFO] Task started: fastANI
[2024-01-24 11:45:17,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg44071e9b-5b74-4bb3-9e4e-d3eeedcdb833/GCF_003173595.1_ASM317359v1_genomic.fna.gz --refList GCF_003173595.1_ASM317359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003173595.1_ASM317359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:31,005] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:31,016] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:31,017] [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_003173595.1	s__Pedobacter yonginense	100.0	1452	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003173575.1	s__Pedobacter paludis	82.5713	940	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306625.1	s__Pedobacter sp014306625	82.4935	950	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331675.1	s__Pedobacter sp004331675	80.4753	636	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708285.2	s__Pedobacter borealis	80.1681	605	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310665.1	s__Pedobacter kyonggii	80.0676	615	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613605.1	s__Pedobacter sp018613605	80.0504	618	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_004335085.1	s__Pedobacter nototheniae	79.9716	560	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.28	98.28	0.90	0.90	2	-
GCF_014635725.1	s__Pedobacter mendelii	79.9281	610	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342125.1	s__Pedobacter sp004342125	79.9117	608	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_003664035.1	s__Pedobacter alluvionis	79.8454	606	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003725795.1	s__Pedobacter jejuensis	79.6657	621	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210715.1	s__Pedobacter sp004210715	79.2979	396	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:31,018] [INFO] GTDB search result was written to GCF_003173595.1_ASM317359v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:31,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:31,022] [INFO] DFAST_QC result json was written to GCF_003173595.1_ASM317359v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:31,022] [INFO] DFAST_QC completed!
[2024-01-24 11:45:31,022] [INFO] Total running time: 0h1m38s