[2024-01-25 18:48:20,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:20,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:20,613] [INFO] DQC Reference Directory: /var/lib/cwl/stgda8760e7-3195-49d7-a9dd-fd04b5129324/dqc_reference
[2024-01-25 18:48:21,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:21,723] [INFO] Task started: Prodigal
[2024-01-25 18:48:21,724] [INFO] Running command: gunzip -c /var/lib/cwl/stge8abeb65-0421-40df-a6b5-773c6c785778/GCF_016775475.1_ASM1677547v1_genomic.fna.gz | prodigal -d GCF_016775475.1_ASM1677547v1_genomic.fna/cds.fna -a GCF_016775475.1_ASM1677547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:38,408] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:38,408] [INFO] Task started: HMMsearch
[2024-01-25 18:48:38,409] [INFO] Running command: hmmsearch --tblout GCF_016775475.1_ASM1677547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda8760e7-3195-49d7-a9dd-fd04b5129324/dqc_reference/reference_markers.hmm GCF_016775475.1_ASM1677547v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:38,707] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:38,708] [INFO] Found 6/6 markers.
[2024-01-25 18:48:38,761] [INFO] Query marker FASTA was written to GCF_016775475.1_ASM1677547v1_genomic.fna/markers.fasta
[2024-01-25 18:48:38,762] [INFO] Task started: Blastn
[2024-01-25 18:48:38,762] [INFO] Running command: blastn -query GCF_016775475.1_ASM1677547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda8760e7-3195-49d7-a9dd-fd04b5129324/dqc_reference/reference_markers.fasta -out GCF_016775475.1_ASM1677547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:39,604] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:39,607] [INFO] Selected 11 target genomes.
[2024-01-25 18:48:39,608] [INFO] Target genome list was writen to GCF_016775475.1_ASM1677547v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:39,615] [INFO] Task started: fastANI
[2024-01-25 18:48:39,615] [INFO] Running command: fastANI --query /var/lib/cwl/stge8abeb65-0421-40df-a6b5-773c6c785778/GCF_016775475.1_ASM1677547v1_genomic.fna.gz --refList GCF_016775475.1_ASM1677547v1_genomic.fna/target_genomes.txt --output GCF_016775475.1_ASM1677547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:55,312] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:55,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda8760e7-3195-49d7-a9dd-fd04b5129324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:55,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda8760e7-3195-49d7-a9dd-fd04b5129324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:55,320] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:48:55,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:55,320] [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
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	100.0	2094	2096	95	conclusive
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	86.4169	1373	2096	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	86.2762	1372	2096	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	85.8368	1427	2096	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	85.711	1379	2096	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	81.9925	1140	2096	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.9791	674	2096	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.781	672	2096	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.5599	709	2096	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.5393	669	2096	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.9955	648	2096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:55,322] [INFO] DFAST Taxonomy check result was written to GCF_016775475.1_ASM1677547v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:55,323] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:55,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:55,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda8760e7-3195-49d7-a9dd-fd04b5129324/dqc_reference/checkm_data
[2024-01-25 18:48:55,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:55,382] [INFO] Task started: CheckM
[2024-01-25 18:48:55,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016775475.1_ASM1677547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016775475.1_ASM1677547v1_genomic.fna/checkm_input GCF_016775475.1_ASM1677547v1_genomic.fna/checkm_result
[2024-01-25 18:49:52,362] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:52,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:52,398] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:52,398] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:52,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016775475.1_ASM1677547v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:52,400] [INFO] Task started: Blastn
[2024-01-25 18:49:52,400] [INFO] Running command: blastn -query GCF_016775475.1_ASM1677547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda8760e7-3195-49d7-a9dd-fd04b5129324/dqc_reference/reference_markers_gtdb.fasta -out GCF_016775475.1_ASM1677547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:54,151] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:54,155] [INFO] Selected 7 target genomes.
[2024-01-25 18:49:54,155] [INFO] Target genome list was writen to GCF_016775475.1_ASM1677547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:54,164] [INFO] Task started: fastANI
[2024-01-25 18:49:54,165] [INFO] Running command: fastANI --query /var/lib/cwl/stge8abeb65-0421-40df-a6b5-773c6c785778/GCF_016775475.1_ASM1677547v1_genomic.fna.gz --refList GCF_016775475.1_ASM1677547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016775475.1_ASM1677547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:06,512] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:06,518] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:06,518] [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_016775475.1	s__Belnapia sp016775475	100.0	2094	2096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101615.1	s__Belnapia rosea	86.2827	1371	2096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	98.36	98.36	0.89	0.89	2	-
GCA_902805545.1	s__Belnapia sp902805545	86.2449	1148	2096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802185.1	s__Belnapia sp000802185	86.0267	1371	2096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016773205.1	s__Belnapia sp016773205	85.8134	1429	2096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745835.1	s__Belnapia moabensis	85.6953	1380	2096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	82.418	1117	2096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:06,520] [INFO] GTDB search result was written to GCF_016775475.1_ASM1677547v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:06,521] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:06,524] [INFO] DFAST_QC result json was written to GCF_016775475.1_ASM1677547v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:06,524] [INFO] DFAST_QC completed!
[2024-01-25 18:50:06,524] [INFO] Total running time: 0h1m46s