[2023-06-13 09:12:09,617] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:12:09,620] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:12:09,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7e5d730-82c4-40f5-88f9-1bde8d1f9916/dqc_reference
[2023-06-13 09:12:10,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:12:10,908] [INFO] Task started: Prodigal
[2023-06-13 09:12:10,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe965939-a6f8-4a07-930a-3f4fc1fbf476/GCA_947459945.1_RE-20apr16-169_genomic.fna.gz | prodigal -d GCA_947459945.1_RE-20apr16-169_genomic.fna/cds.fna -a GCA_947459945.1_RE-20apr16-169_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:12:20,823] [INFO] Task succeeded: Prodigal
[2023-06-13 09:12:20,823] [INFO] Task started: HMMsearch
[2023-06-13 09:12:20,824] [INFO] Running command: hmmsearch --tblout GCA_947459945.1_RE-20apr16-169_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7e5d730-82c4-40f5-88f9-1bde8d1f9916/dqc_reference/reference_markers.hmm GCA_947459945.1_RE-20apr16-169_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:12:20,977] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:12:20,978] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgfe965939-a6f8-4a07-930a-3f4fc1fbf476/GCA_947459945.1_RE-20apr16-169_genomic.fna.gz]
[2023-06-13 09:12:20,997] [INFO] Query marker FASTA was written to GCA_947459945.1_RE-20apr16-169_genomic.fna/markers.fasta
[2023-06-13 09:12:20,998] [INFO] Task started: Blastn
[2023-06-13 09:12:20,998] [INFO] Running command: blastn -query GCA_947459945.1_RE-20apr16-169_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7e5d730-82c4-40f5-88f9-1bde8d1f9916/dqc_reference/reference_markers.fasta -out GCA_947459945.1_RE-20apr16-169_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:21,513] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:21,516] [INFO] Selected 5 target genomes.
[2023-06-13 09:12:21,517] [INFO] Target genome list was writen to GCA_947459945.1_RE-20apr16-169_genomic.fna/target_genomes.txt
[2023-06-13 09:12:21,518] [INFO] Task started: fastANI
[2023-06-13 09:12:21,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe965939-a6f8-4a07-930a-3f4fc1fbf476/GCA_947459945.1_RE-20apr16-169_genomic.fna.gz --refList GCA_947459945.1_RE-20apr16-169_genomic.fna/target_genomes.txt --output GCA_947459945.1_RE-20apr16-169_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:25,015] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:25,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7e5d730-82c4-40f5-88f9-1bde8d1f9916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:25,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7e5d730-82c4-40f5-88f9-1bde8d1f9916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:25,023] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:12:25,023] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:12:25,023] [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
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	76.9007	123	572	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	76.5444	88	572	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	76.5422	73	572	95	below_threshold
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	76.405	92	572	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	76.1434	105	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:12:25,029] [INFO] DFAST Taxonomy check result was written to GCA_947459945.1_RE-20apr16-169_genomic.fna/tc_result.tsv
[2023-06-13 09:12:25,030] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:25,030] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:25,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7e5d730-82c4-40f5-88f9-1bde8d1f9916/dqc_reference/checkm_data
[2023-06-13 09:12:25,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:25,058] [INFO] Task started: CheckM
[2023-06-13 09:12:25,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947459945.1_RE-20apr16-169_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947459945.1_RE-20apr16-169_genomic.fna/checkm_input GCA_947459945.1_RE-20apr16-169_genomic.fna/checkm_result
[2023-06-13 09:12:57,973] [INFO] Task succeeded: CheckM
[2023-06-13 09:12:57,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:12:57,988] [INFO] ===== Completeness check finished =====
[2023-06-13 09:12:57,988] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:12:57,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947459945.1_RE-20apr16-169_genomic.fna/markers.fasta)
[2023-06-13 09:12:57,989] [INFO] Task started: Blastn
[2023-06-13 09:12:57,989] [INFO] Running command: blastn -query GCA_947459945.1_RE-20apr16-169_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7e5d730-82c4-40f5-88f9-1bde8d1f9916/dqc_reference/reference_markers_gtdb.fasta -out GCA_947459945.1_RE-20apr16-169_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:58,564] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:58,568] [INFO] Selected 7 target genomes.
[2023-06-13 09:12:58,568] [INFO] Target genome list was writen to GCA_947459945.1_RE-20apr16-169_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:12:58,570] [INFO] Task started: fastANI
[2023-06-13 09:12:58,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe965939-a6f8-4a07-930a-3f4fc1fbf476/GCA_947459945.1_RE-20apr16-169_genomic.fna.gz --refList GCA_947459945.1_RE-20apr16-169_genomic.fna/target_genomes_gtdb.txt --output GCA_947459945.1_RE-20apr16-169_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:13:02,393] [INFO] Task succeeded: fastANI
[2023-06-13 09:13:02,400] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 09:13:02,400] [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
GCA_005788235.1	s__Algoriphagus sp005788235	89.0192	400	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952135.1	s__Algoriphagus sp903952135	84.1965	427	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
GCF_003253485.1	s__Algoriphagus aquaeductus	76.9007	123	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	76.8419	123	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	76.7725	131	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:13:02,403] [INFO] GTDB search result was written to GCA_947459945.1_RE-20apr16-169_genomic.fna/result_gtdb.tsv
[2023-06-13 09:13:02,404] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:13:02,406] [INFO] DFAST_QC result json was written to GCA_947459945.1_RE-20apr16-169_genomic.fna/dqc_result.json
[2023-06-13 09:13:02,407] [INFO] DFAST_QC completed!
[2023-06-13 09:13:02,407] [INFO] Total running time: 0h0m53s