[2023-06-13 00:45:23,209] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:45:23,211] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:45:23,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c9fc4a2-43aa-4417-8060-6f2cd80097a8/dqc_reference
[2023-06-13 00:45:24,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:45:24,458] [INFO] Task started: Prodigal
[2023-06-13 00:45:24,458] [INFO] Running command: gunzip -c /var/lib/cwl/stga17b1fed-4b3f-40ef-a186-29907e18cb26/GCA_022563575.1_ASM2256357v1_genomic.fna.gz | prodigal -d GCA_022563575.1_ASM2256357v1_genomic.fna/cds.fna -a GCA_022563575.1_ASM2256357v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:45:33,250] [INFO] Task succeeded: Prodigal
[2023-06-13 00:45:33,251] [INFO] Task started: HMMsearch
[2023-06-13 00:45:33,251] [INFO] Running command: hmmsearch --tblout GCA_022563575.1_ASM2256357v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c9fc4a2-43aa-4417-8060-6f2cd80097a8/dqc_reference/reference_markers.hmm GCA_022563575.1_ASM2256357v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:45:33,543] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:45:33,544] [INFO] Found 6/6 markers.
[2023-06-13 00:45:33,593] [INFO] Query marker FASTA was written to GCA_022563575.1_ASM2256357v1_genomic.fna/markers.fasta
[2023-06-13 00:45:33,594] [INFO] Task started: Blastn
[2023-06-13 00:45:33,594] [INFO] Running command: blastn -query GCA_022563575.1_ASM2256357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c9fc4a2-43aa-4417-8060-6f2cd80097a8/dqc_reference/reference_markers.fasta -out GCA_022563575.1_ASM2256357v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:34,297] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:34,306] [INFO] Selected 30 target genomes.
[2023-06-13 00:45:34,307] [INFO] Target genome list was writen to GCA_022563575.1_ASM2256357v1_genomic.fna/target_genomes.txt
[2023-06-13 00:45:34,312] [INFO] Task started: fastANI
[2023-06-13 00:45:34,313] [INFO] Running command: fastANI --query /var/lib/cwl/stga17b1fed-4b3f-40ef-a186-29907e18cb26/GCA_022563575.1_ASM2256357v1_genomic.fna.gz --refList GCA_022563575.1_ASM2256357v1_genomic.fna/target_genomes.txt --output GCA_022563575.1_ASM2256357v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:45:58,532] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:58,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c9fc4a2-43aa-4417-8060-6f2cd80097a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:45:58,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c9fc4a2-43aa-4417-8060-6f2cd80097a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:45:58,534] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:45:58,534] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 00:45:58,534] [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 00:45:58,536] [INFO] DFAST Taxonomy check result was written to GCA_022563575.1_ASM2256357v1_genomic.fna/tc_result.tsv
[2023-06-13 00:45:58,536] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:45:58,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:45:58,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c9fc4a2-43aa-4417-8060-6f2cd80097a8/dqc_reference/checkm_data
[2023-06-13 00:45:58,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:45:58,591] [INFO] Task started: CheckM
[2023-06-13 00:45:58,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022563575.1_ASM2256357v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022563575.1_ASM2256357v1_genomic.fna/checkm_input GCA_022563575.1_ASM2256357v1_genomic.fna/checkm_result
[2023-06-13 00:46:29,004] [INFO] Task succeeded: CheckM
[2023-06-13 00:46:29,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.44%
Contamintation: 6.48%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-06-13 00:46:29,036] [INFO] ===== Completeness check finished =====
[2023-06-13 00:46:29,036] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:46:29,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022563575.1_ASM2256357v1_genomic.fna/markers.fasta)
[2023-06-13 00:46:29,037] [INFO] Task started: Blastn
[2023-06-13 00:46:29,037] [INFO] Running command: blastn -query GCA_022563575.1_ASM2256357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c9fc4a2-43aa-4417-8060-6f2cd80097a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022563575.1_ASM2256357v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:46:30,125] [INFO] Task succeeded: Blastn
[2023-06-13 00:46:30,130] [INFO] Selected 28 target genomes.
[2023-06-13 00:46:30,131] [INFO] Target genome list was writen to GCA_022563575.1_ASM2256357v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:46:30,149] [INFO] Task started: fastANI
[2023-06-13 00:46:30,149] [INFO] Running command: fastANI --query /var/lib/cwl/stga17b1fed-4b3f-40ef-a186-29907e18cb26/GCA_022563575.1_ASM2256357v1_genomic.fna.gz --refList GCA_022563575.1_ASM2256357v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022563575.1_ASM2256357v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:46:46,601] [INFO] Task succeeded: fastANI
[2023-06-13 00:46:46,612] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 00:46:46,613] [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_900696525.1	s__CAADGL01 sp900696525	76.4151	63	664	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__CAADGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162245.1	s__Fen-1342 sp003162245	76.3224	51	664	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__Fen-1342	95.0	99.89	99.89	0.96	0.96	2	-
GCA_011054455.1	s__DSPM01 sp011054455	75.9753	57	664	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__DSPM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999985.1	s__JAGNKU01 sp017999985	75.8445	68	664	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__JAGNKU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018814045.1	s__JAHJAR01 sp018814045	75.8273	70	664	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__JAHJAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859745.1	s__RAS1 sp007859745	75.7716	76	664	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__RAS1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:46:46,615] [INFO] GTDB search result was written to GCA_022563575.1_ASM2256357v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:46:46,615] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:46:46,618] [INFO] DFAST_QC result json was written to GCA_022563575.1_ASM2256357v1_genomic.fna/dqc_result.json
[2023-06-13 00:46:46,618] [INFO] DFAST_QC completed!
[2023-06-13 00:46:46,618] [INFO] Total running time: 0h1m23s