[2024-01-24 13:12:54,425] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:54,427] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:54,427] [INFO] DQC Reference Directory: /var/lib/cwl/stga3d1f1fb-cb4d-4ab3-ba3c-3e46cb9a7268/dqc_reference
[2024-01-24 13:12:55,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:55,781] [INFO] Task started: Prodigal
[2024-01-24 13:12:55,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgda3f83f0-032e-47a6-b6dd-2da32502c7b7/GCF_010119225.1_ASM1011922v1_genomic.fna.gz | prodigal -d GCF_010119225.1_ASM1011922v1_genomic.fna/cds.fna -a GCF_010119225.1_ASM1011922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:23,642] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:23,643] [INFO] Task started: HMMsearch
[2024-01-24 13:13:23,643] [INFO] Running command: hmmsearch --tblout GCF_010119225.1_ASM1011922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3d1f1fb-cb4d-4ab3-ba3c-3e46cb9a7268/dqc_reference/reference_markers.hmm GCF_010119225.1_ASM1011922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:23,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:23,964] [INFO] Found 6/6 markers.
[2024-01-24 13:13:24,012] [INFO] Query marker FASTA was written to GCF_010119225.1_ASM1011922v1_genomic.fna/markers.fasta
[2024-01-24 13:13:24,013] [INFO] Task started: Blastn
[2024-01-24 13:13:24,013] [INFO] Running command: blastn -query GCF_010119225.1_ASM1011922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d1f1fb-cb4d-4ab3-ba3c-3e46cb9a7268/dqc_reference/reference_markers.fasta -out GCF_010119225.1_ASM1011922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:24,612] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:24,616] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:24,616] [INFO] Target genome list was writen to GCF_010119225.1_ASM1011922v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:24,629] [INFO] Task started: fastANI
[2024-01-24 13:13:24,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgda3f83f0-032e-47a6-b6dd-2da32502c7b7/GCF_010119225.1_ASM1011922v1_genomic.fna.gz --refList GCF_010119225.1_ASM1011922v1_genomic.fna/target_genomes.txt --output GCF_010119225.1_ASM1011922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:38,765] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:38,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3d1f1fb-cb4d-4ab3-ba3c-3e46cb9a7268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:38,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3d1f1fb-cb4d-4ab3-ba3c-3e46cb9a7268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:38,774] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:38,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:38,774] [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
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	100.0	1861	1862	95	conclusive
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	94.0451	1636	1862	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	85.9378	1479	1862	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	80.7669	866	1862	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	79.8596	784	1862	95	below_threshold
Cyclobacterium lianum	strain=CGMCC 1.6102	GCA_900143075.1	388280	388280	type	True	78.7595	558	1862	95	below_threshold
Cyclobacterium marinum	strain=DSM 745	GCA_000222485.1	104	104	type	True	77.3181	225	1862	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	76.2902	85	1862	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	75.7917	56	1862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,775] [INFO] DFAST Taxonomy check result was written to GCF_010119225.1_ASM1011922v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:38,776] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:38,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:38,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3d1f1fb-cb4d-4ab3-ba3c-3e46cb9a7268/dqc_reference/checkm_data
[2024-01-24 13:13:38,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:38,834] [INFO] Task started: CheckM
[2024-01-24 13:13:38,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119225.1_ASM1011922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119225.1_ASM1011922v1_genomic.fna/checkm_input GCF_010119225.1_ASM1011922v1_genomic.fna/checkm_result
[2024-01-24 13:14:54,397] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:54,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:54,442] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:54,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:54,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119225.1_ASM1011922v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:54,444] [INFO] Task started: Blastn
[2024-01-24 13:14:54,444] [INFO] Running command: blastn -query GCF_010119225.1_ASM1011922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d1f1fb-cb4d-4ab3-ba3c-3e46cb9a7268/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119225.1_ASM1011922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:55,354] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:55,358] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:55,358] [INFO] Target genome list was writen to GCF_010119225.1_ASM1011922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:55,367] [INFO] Task started: fastANI
[2024-01-24 13:14:55,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgda3f83f0-032e-47a6-b6dd-2da32502c7b7/GCF_010119225.1_ASM1011922v1_genomic.fna.gz --refList GCF_010119225.1_ASM1011922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119225.1_ASM1011922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:11,246] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:11,263] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:11,263] [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_010119225.1	s__Cyclobacterium sp010119225	100.0	1861	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010119245.1	s__Cyclobacterium sp010119245	94.0451	1636	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	85.9377	1479	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	82.8191	861	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009467825.1	s__Cyclobacterium xiamenense	80.753	868	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCF_011290685.1	s__Cyclobacterium plantarum	79.87	782	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	79.1709	707	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143075.1	s__Cyclobacterium lianum	78.7548	559	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	76.2902	85	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373065.1	s__Algoriphagus sp013373065	76.05	50	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373335.1	s__Algoriphagus sp013373335	75.8991	52	1862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:11,265] [INFO] GTDB search result was written to GCF_010119225.1_ASM1011922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:11,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:11,268] [INFO] DFAST_QC result json was written to GCF_010119225.1_ASM1011922v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:11,268] [INFO] DFAST_QC completed!
[2024-01-24 13:15:11,269] [INFO] Total running time: 0h2m17s