[2024-01-24 14:12:16,025] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:16,036] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:16,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgd62c7b76-267d-45ce-9b11-f909049fc653/dqc_reference
[2024-01-24 14:12:17,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:17,310] [INFO] Task started: Prodigal
[2024-01-24 14:12:17,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg374ae3d6-20ae-4fee-b259-c005bdb43ca7/GCF_005116505.1_ASM511650v1_genomic.fna.gz | prodigal -d GCF_005116505.1_ASM511650v1_genomic.fna/cds.fna -a GCF_005116505.1_ASM511650v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:33,276] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:33,277] [INFO] Task started: HMMsearch
[2024-01-24 14:12:33,277] [INFO] Running command: hmmsearch --tblout GCF_005116505.1_ASM511650v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd62c7b76-267d-45ce-9b11-f909049fc653/dqc_reference/reference_markers.hmm GCF_005116505.1_ASM511650v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:33,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:33,688] [INFO] Found 6/6 markers.
[2024-01-24 14:12:33,731] [INFO] Query marker FASTA was written to GCF_005116505.1_ASM511650v1_genomic.fna/markers.fasta
[2024-01-24 14:12:33,732] [INFO] Task started: Blastn
[2024-01-24 14:12:33,732] [INFO] Running command: blastn -query GCF_005116505.1_ASM511650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd62c7b76-267d-45ce-9b11-f909049fc653/dqc_reference/reference_markers.fasta -out GCF_005116505.1_ASM511650v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:34,386] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:34,389] [INFO] Selected 13 target genomes.
[2024-01-24 14:12:34,390] [INFO] Target genome list was writen to GCF_005116505.1_ASM511650v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:34,404] [INFO] Task started: fastANI
[2024-01-24 14:12:34,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg374ae3d6-20ae-4fee-b259-c005bdb43ca7/GCF_005116505.1_ASM511650v1_genomic.fna.gz --refList GCF_005116505.1_ASM511650v1_genomic.fna/target_genomes.txt --output GCF_005116505.1_ASM511650v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:46,556] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:46,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd62c7b76-267d-45ce-9b11-f909049fc653/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:46,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd62c7b76-267d-45ce-9b11-f909049fc653/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:46,574] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:46,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:46,574] [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 polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	100.0	1516	1518	95	conclusive
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	81.7207	900	1518	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	81.1115	735	1518	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	80.8988	734	1518	95	below_threshold
Pedobacter insulae	strain=DSM 18684	GCA_900113525.1	414048	414048	type	True	78.7614	407	1518	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.1787	232	1518	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	78.1328	350	1518	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	77.9204	309	1518	95	below_threshold
Pedobacter metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	77.8715	191	1518	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.5814	235	1518	95	below_threshold
Pedobacter rhizosphaerae	strain=DSM 18610	GCA_900111155.1	390241	390241	type	True	77.5332	235	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:46,576] [INFO] DFAST Taxonomy check result was written to GCF_005116505.1_ASM511650v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:46,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:46,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:46,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd62c7b76-267d-45ce-9b11-f909049fc653/dqc_reference/checkm_data
[2024-01-24 14:12:46,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:46,626] [INFO] Task started: CheckM
[2024-01-24 14:12:46,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116505.1_ASM511650v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116505.1_ASM511650v1_genomic.fna/checkm_input GCF_005116505.1_ASM511650v1_genomic.fna/checkm_result
[2024-01-24 14:13:32,857] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:32,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:32,880] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:32,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:32,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116505.1_ASM511650v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:32,881] [INFO] Task started: Blastn
[2024-01-24 14:13:32,882] [INFO] Running command: blastn -query GCF_005116505.1_ASM511650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd62c7b76-267d-45ce-9b11-f909049fc653/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116505.1_ASM511650v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:33,677] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:33,681] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:33,682] [INFO] Target genome list was writen to GCF_005116505.1_ASM511650v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:33,729] [INFO] Task started: fastANI
[2024-01-24 14:13:33,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg374ae3d6-20ae-4fee-b259-c005bdb43ca7/GCF_005116505.1_ASM511650v1_genomic.fna.gz --refList GCF_005116505.1_ASM511650v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116505.1_ASM511650v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:42,673] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:42,686] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:42,686] [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_005116505.1	s__Pedobacter sp005116505	100.0	1516	1518	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_004331645.1	s__Pedobacter sp004331645	81.7128	901	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	81.1258	734	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116475.1	s__Pedobacter sp005116475	80.9023	734	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204825.1	s__Pedobacter boryungensis	80.7254	664	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412215.1	s__Pedobacter sp001412215	79.7719	601	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377775.1	s__Pedobacter sp014377775	78.5777	379	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215335.1	s__Pedobacter xixiisoli	78.1542	348	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005925345.1	s__Pedobacter ureilyticus	77.9415	307	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362715.1	s__Pedobacter metabolipauper	77.8692	190	1518	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 14:13:42,688] [INFO] GTDB search result was written to GCF_005116505.1_ASM511650v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:42,689] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:42,692] [INFO] DFAST_QC result json was written to GCF_005116505.1_ASM511650v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:42,692] [INFO] DFAST_QC completed!
[2024-01-24 14:13:42,692] [INFO] Total running time: 0h1m27s