[2024-01-24 13:31:11,632] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:11,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:11,634] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd9fa944-5aae-40a2-85be-56082e665337/dqc_reference
[2024-01-24 13:31:12,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:12,820] [INFO] Task started: Prodigal
[2024-01-24 13:31:12,820] [INFO] Running command: gunzip -c /var/lib/cwl/stgc59ee0c8-bd4a-4e85-8bac-3c0586e1acf4/GCF_001028705.1_ASM102870v1_genomic.fna.gz | prodigal -d GCF_001028705.1_ASM102870v1_genomic.fna/cds.fna -a GCF_001028705.1_ASM102870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:24,741] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:24,741] [INFO] Task started: HMMsearch
[2024-01-24 13:31:24,741] [INFO] Running command: hmmsearch --tblout GCF_001028705.1_ASM102870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd9fa944-5aae-40a2-85be-56082e665337/dqc_reference/reference_markers.hmm GCF_001028705.1_ASM102870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:24,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:24,942] [INFO] Found 6/6 markers.
[2024-01-24 13:31:24,974] [INFO] Query marker FASTA was written to GCF_001028705.1_ASM102870v1_genomic.fna/markers.fasta
[2024-01-24 13:31:24,974] [INFO] Task started: Blastn
[2024-01-24 13:31:24,975] [INFO] Running command: blastn -query GCF_001028705.1_ASM102870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd9fa944-5aae-40a2-85be-56082e665337/dqc_reference/reference_markers.fasta -out GCF_001028705.1_ASM102870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:25,832] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:25,835] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:25,835] [INFO] Target genome list was writen to GCF_001028705.1_ASM102870v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:25,840] [INFO] Task started: fastANI
[2024-01-24 13:31:25,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59ee0c8-bd4a-4e85-8bac-3c0586e1acf4/GCF_001028705.1_ASM102870v1_genomic.fna.gz --refList GCF_001028705.1_ASM102870v1_genomic.fna/target_genomes.txt --output GCF_001028705.1_ASM102870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:35,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:35,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd9fa944-5aae-40a2-85be-56082e665337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:35,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd9fa944-5aae-40a2-85be-56082e665337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:35,910] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:35,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:35,910] [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
Croceicoccus naphthovorans	strain=PQ-2	GCA_001028705.1	1348774	1348774	type	True	100.0	1283	1286	95	conclusive
Croceicoccus naphthovorans	strain=DSM 102796	GCA_014196855.1	1348774	1348774	type	True	99.9368	1217	1286	95	conclusive
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	82.7947	650	1286	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	82.051	631	1286	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	82.0249	617	1286	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	81.7959	647	1286	95	below_threshold
Croceicoccus pelagius	strain=CGMCC 1.15358	GCA_014642495.1	1703341	1703341	type	True	81.72	642	1286	95	below_threshold
Croceicoccus ponticola	strain=GM-16	GCA_004004515.1	2217664	2217664	type	True	81.0824	546	1286	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	79.7598	361	1286	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	79.7494	361	1286	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	79.4134	389	1286	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.2296	334	1286	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.6357	324	1286	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.5806	259	1286	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.9852	231	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:35,912] [INFO] DFAST Taxonomy check result was written to GCF_001028705.1_ASM102870v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:35,912] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:35,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:35,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd9fa944-5aae-40a2-85be-56082e665337/dqc_reference/checkm_data
[2024-01-24 13:31:35,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:35,950] [INFO] Task started: CheckM
[2024-01-24 13:31:35,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001028705.1_ASM102870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001028705.1_ASM102870v1_genomic.fna/checkm_input GCF_001028705.1_ASM102870v1_genomic.fna/checkm_result
[2024-01-24 13:32:13,760] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:13,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:13,780] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:13,781] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:13,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001028705.1_ASM102870v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:13,781] [INFO] Task started: Blastn
[2024-01-24 13:32:13,781] [INFO] Running command: blastn -query GCF_001028705.1_ASM102870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd9fa944-5aae-40a2-85be-56082e665337/dqc_reference/reference_markers_gtdb.fasta -out GCF_001028705.1_ASM102870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:15,425] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:15,429] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:15,430] [INFO] Target genome list was writen to GCF_001028705.1_ASM102870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:15,456] [INFO] Task started: fastANI
[2024-01-24 13:32:15,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59ee0c8-bd4a-4e85-8bac-3c0586e1acf4/GCF_001028705.1_ASM102870v1_genomic.fna.gz --refList GCF_001028705.1_ASM102870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001028705.1_ASM102870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:23,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:23,854] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:23,854] [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_001028705.1	s__Croceicoccus naphthovorans	100.0	1282	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001634625.1	s__Croceicoccus bisphenolivorans	82.7947	650	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398395.1	s__Croceicoccus sp018398395	82.0359	633	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570835.1	s__Croceicoccus sediminis	82.0335	616	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661915.1	s__Croceicoccus pelagius	81.781	651	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004004515.1	s__Croceicoccus ponticola	81.106	544	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661965.1	s__Croceicoccus mobilis	80.3134	496	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013408095.1	s__Novosphingobium marinum	79.8081	358	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.6502	400	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	78.3756	259	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011054555.1	s__Erythrobacter sp011054555	77.8518	224	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:23,856] [INFO] GTDB search result was written to GCF_001028705.1_ASM102870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:23,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:23,860] [INFO] DFAST_QC result json was written to GCF_001028705.1_ASM102870v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:23,860] [INFO] DFAST_QC completed!
[2024-01-24 13:32:23,861] [INFO] Total running time: 0h1m12s