[2024-01-24 14:05:46,377] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:46,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:46,379] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9446c38-d373-4e4b-b769-41948dd6ccf8/dqc_reference
[2024-01-24 14:05:47,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:47,663] [INFO] Task started: Prodigal
[2024-01-24 14:05:47,663] [INFO] Running command: gunzip -c /var/lib/cwl/stgd17b3676-6972-4a92-a223-cff8998f325e/GCF_003231495.1_AcaThom1.0_genomic.fna.gz | prodigal -d GCF_003231495.1_AcaThom1.0_genomic.fna/cds.fna -a GCF_003231495.1_AcaThom1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:02,467] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:02,468] [INFO] Task started: HMMsearch
[2024-01-24 14:06:02,468] [INFO] Running command: hmmsearch --tblout GCF_003231495.1_AcaThom1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9446c38-d373-4e4b-b769-41948dd6ccf8/dqc_reference/reference_markers.hmm GCF_003231495.1_AcaThom1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:02,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:02,842] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd17b3676-6972-4a92-a223-cff8998f325e/GCF_003231495.1_AcaThom1.0_genomic.fna.gz]
[2024-01-24 14:06:02,891] [INFO] Query marker FASTA was written to GCF_003231495.1_AcaThom1.0_genomic.fna/markers.fasta
[2024-01-24 14:06:02,891] [INFO] Task started: Blastn
[2024-01-24 14:06:02,892] [INFO] Running command: blastn -query GCF_003231495.1_AcaThom1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9446c38-d373-4e4b-b769-41948dd6ccf8/dqc_reference/reference_markers.fasta -out GCF_003231495.1_AcaThom1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:03,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:03,506] [INFO] Selected 31 target genomes.
[2024-01-24 14:06:03,507] [INFO] Target genome list was writen to GCF_003231495.1_AcaThom1.0_genomic.fna/target_genomes.txt
[2024-01-24 14:06:03,519] [INFO] Task started: fastANI
[2024-01-24 14:06:03,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgd17b3676-6972-4a92-a223-cff8998f325e/GCF_003231495.1_AcaThom1.0_genomic.fna.gz --refList GCF_003231495.1_AcaThom1.0_genomic.fna/target_genomes.txt --output GCF_003231495.1_AcaThom1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:26,958] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:26,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9446c38-d373-4e4b-b769-41948dd6ccf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:26,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9446c38-d373-4e4b-b769-41948dd6ccf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:26,963] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:26,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:26,964] [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
Acaryochloris thomasi	strain=RCC1774	GCA_003231495.1	2929456	2929456	type	True	100.0	1937	1939	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,965] [INFO] DFAST Taxonomy check result was written to GCF_003231495.1_AcaThom1.0_genomic.fna/tc_result.tsv
[2024-01-24 14:06:26,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:26,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:26,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9446c38-d373-4e4b-b769-41948dd6ccf8/dqc_reference/checkm_data
[2024-01-24 14:06:26,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:27,033] [INFO] Task started: CheckM
[2024-01-24 14:06:27,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003231495.1_AcaThom1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003231495.1_AcaThom1.0_genomic.fna/checkm_input GCF_003231495.1_AcaThom1.0_genomic.fna/checkm_result
[2024-01-24 14:07:14,122] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:14,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,144] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:14,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:14,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003231495.1_AcaThom1.0_genomic.fna/markers.fasta)
[2024-01-24 14:07:14,145] [INFO] Task started: Blastn
[2024-01-24 14:07:14,145] [INFO] Running command: blastn -query GCF_003231495.1_AcaThom1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9446c38-d373-4e4b-b769-41948dd6ccf8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003231495.1_AcaThom1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:14,904] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:14,908] [INFO] Selected 33 target genomes.
[2024-01-24 14:07:14,908] [INFO] Target genome list was writen to GCF_003231495.1_AcaThom1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:14,956] [INFO] Task started: fastANI
[2024-01-24 14:07:14,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgd17b3676-6972-4a92-a223-cff8998f325e/GCF_003231495.1_AcaThom1.0_genomic.fna.gz --refList GCF_003231495.1_AcaThom1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_003231495.1_AcaThom1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:45,496] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:45,512] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:45,513] [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_003231495.1	s__RCC1774 sp003231495	100.0	1937	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__RCC1774	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000018105.1	s__Acaryochloris marina	76.4826	104	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Acaryochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034865.1	s__Acaryochloris sp012034865	75.9749	68	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Acaryochloris	95.0	98.65	97.52	0.87	0.83	3	-
GCF_015207395.1	s__Nodosilinea sp015207395	75.9442	60	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696675.1	s__Nodosilinea tenue	75.8649	54	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000309385.1	s__Nodosilinea nodulosa	75.7978	55	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003017855.1	s__Nodosilinea sp003017855	75.7345	56	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
GCF_015207605.1	s__Oculatella sp015207605	75.6171	52	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Oculatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207525.1	s__Nodosilinea sp015207525	75.5999	54	1939	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:45,514] [INFO] GTDB search result was written to GCF_003231495.1_AcaThom1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:45,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:45,517] [INFO] DFAST_QC result json was written to GCF_003231495.1_AcaThom1.0_genomic.fna/dqc_result.json
[2024-01-24 14:07:45,517] [INFO] DFAST_QC completed!
[2024-01-24 14:07:45,518] [INFO] Total running time: 0h1m59s