[2023-06-13 00:45:30,636] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:45:30,638] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:45:30,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg68e6578b-a027-4306-b6a7-5913c3981c44/dqc_reference
[2023-06-13 00:45:33,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:45:33,538] [INFO] Task started: Prodigal
[2023-06-13 00:45:33,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg628eb464-5f03-4023-ac7d-7a35b092f875/GCA_947459765.1_RE-20apr16-222_genomic.fna.gz | prodigal -d GCA_947459765.1_RE-20apr16-222_genomic.fna/cds.fna -a GCA_947459765.1_RE-20apr16-222_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:45:35,402] [INFO] Task succeeded: Prodigal
[2023-06-13 00:45:35,403] [INFO] Task started: HMMsearch
[2023-06-13 00:45:35,403] [INFO] Running command: hmmsearch --tblout GCA_947459765.1_RE-20apr16-222_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68e6578b-a027-4306-b6a7-5913c3981c44/dqc_reference/reference_markers.hmm GCA_947459765.1_RE-20apr16-222_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:45:35,670] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:45:35,671] [INFO] Found 6/6 markers.
[2023-06-13 00:45:35,688] [INFO] Query marker FASTA was written to GCA_947459765.1_RE-20apr16-222_genomic.fna/markers.fasta
[2023-06-13 00:45:35,689] [INFO] Task started: Blastn
[2023-06-13 00:45:35,689] [INFO] Running command: blastn -query GCA_947459765.1_RE-20apr16-222_genomic.fna/markers.fasta -db /var/lib/cwl/stg68e6578b-a027-4306-b6a7-5913c3981c44/dqc_reference/reference_markers.fasta -out GCA_947459765.1_RE-20apr16-222_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:39,209] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:39,213] [INFO] Selected 25 target genomes.
[2023-06-13 00:45:39,213] [INFO] Target genome list was writen to GCA_947459765.1_RE-20apr16-222_genomic.fna/target_genomes.txt
[2023-06-13 00:45:39,222] [INFO] Task started: fastANI
[2023-06-13 00:45:39,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg628eb464-5f03-4023-ac7d-7a35b092f875/GCA_947459765.1_RE-20apr16-222_genomic.fna.gz --refList GCA_947459765.1_RE-20apr16-222_genomic.fna/target_genomes.txt --output GCA_947459765.1_RE-20apr16-222_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:45:52,367] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:52,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68e6578b-a027-4306-b6a7-5913c3981c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:45:52,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68e6578b-a027-4306-b6a7-5913c3981c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:45:52,370] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:45:52,370] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 00:45:52,370] [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
--------------------------------------------------------------------------------
[2023-06-13 00:45:52,382] [INFO] DFAST Taxonomy check result was written to GCA_947459765.1_RE-20apr16-222_genomic.fna/tc_result.tsv
[2023-06-13 00:45:52,383] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:45:52,383] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:45:52,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68e6578b-a027-4306-b6a7-5913c3981c44/dqc_reference/checkm_data
[2023-06-13 00:45:52,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:45:52,414] [INFO] Task started: CheckM
[2023-06-13 00:45:52,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947459765.1_RE-20apr16-222_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947459765.1_RE-20apr16-222_genomic.fna/checkm_input GCA_947459765.1_RE-20apr16-222_genomic.fna/checkm_result
[2023-06-13 00:46:07,477] [INFO] Task succeeded: CheckM
[2023-06-13 00:46:07,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:46:07,505] [INFO] ===== Completeness check finished =====
[2023-06-13 00:46:07,505] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:46:07,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947459765.1_RE-20apr16-222_genomic.fna/markers.fasta)
[2023-06-13 00:46:07,506] [INFO] Task started: Blastn
[2023-06-13 00:46:07,506] [INFO] Running command: blastn -query GCA_947459765.1_RE-20apr16-222_genomic.fna/markers.fasta -db /var/lib/cwl/stg68e6578b-a027-4306-b6a7-5913c3981c44/dqc_reference/reference_markers_gtdb.fasta -out GCA_947459765.1_RE-20apr16-222_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:46:08,277] [INFO] Task succeeded: Blastn
[2023-06-13 00:46:08,281] [INFO] Selected 14 target genomes.
[2023-06-13 00:46:08,282] [INFO] Target genome list was writen to GCA_947459765.1_RE-20apr16-222_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:46:08,285] [INFO] Task started: fastANI
[2023-06-13 00:46:08,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg628eb464-5f03-4023-ac7d-7a35b092f875/GCA_947459765.1_RE-20apr16-222_genomic.fna.gz --refList GCA_947459765.1_RE-20apr16-222_genomic.fna/target_genomes_gtdb.txt --output GCA_947459765.1_RE-20apr16-222_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:46:11,497] [INFO] Task succeeded: fastANI
[2023-06-13 00:46:11,513] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:46:11,515] [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_009699825.1	s__Planktophila sp009699825	99.0787	208	245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.12	98.92	0.84	0.84	3	conclusive
GCF_002288365.1	s__Planktophila limnetica	81.993	179	245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.17	97.12	0.96	0.96	5	-
GCA_903890345.1	s__Planktophila sp903890345	81.4598	105	245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.13	96.64	0.70	0.68	4	-
GCA_010032875.1	s__Planktophila sp010032875	81.0381	131	245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.21	99.21	0.88	0.88	2	-
GCA_014190015.1	s__Planktophila sp014190015	81.0341	145	245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009706135.1	s__Planktophila sp009706135	80.9251	116	245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726135.1	s__Planktophila sp009726135	77.219	50	245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.91	99.82	0.93	0.91	6	-
--------------------------------------------------------------------------------
[2023-06-13 00:46:11,517] [INFO] GTDB search result was written to GCA_947459765.1_RE-20apr16-222_genomic.fna/result_gtdb.tsv
[2023-06-13 00:46:11,518] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:46:11,522] [INFO] DFAST_QC result json was written to GCA_947459765.1_RE-20apr16-222_genomic.fna/dqc_result.json
[2023-06-13 00:46:11,522] [INFO] DFAST_QC completed!
[2023-06-13 00:46:11,522] [INFO] Total running time: 0h0m41s