[2023-06-19 03:53:33,830] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:53:33,833] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:53:33,834] [INFO] DQC Reference Directory: /var/lib/cwl/stga24adcd8-1d46-4581-970a-d0adf69b64ef/dqc_reference
[2023-06-19 03:53:35,723] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:53:35,724] [INFO] Task started: Prodigal
[2023-06-19 03:53:35,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg317d5c4b-6fd3-4851-9c65-fa83f9c090cf/GCA_018239665.1_ASM1823966v1_genomic.fna.gz | prodigal -d GCA_018239665.1_ASM1823966v1_genomic.fna/cds.fna -a GCA_018239665.1_ASM1823966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:53:41,920] [INFO] Task succeeded: Prodigal
[2023-06-19 03:53:41,921] [INFO] Task started: HMMsearch
[2023-06-19 03:53:41,921] [INFO] Running command: hmmsearch --tblout GCA_018239665.1_ASM1823966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga24adcd8-1d46-4581-970a-d0adf69b64ef/dqc_reference/reference_markers.hmm GCA_018239665.1_ASM1823966v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:53:42,171] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:53:42,173] [INFO] Found 6/6 markers.
[2023-06-19 03:53:42,209] [INFO] Query marker FASTA was written to GCA_018239665.1_ASM1823966v1_genomic.fna/markers.fasta
[2023-06-19 03:53:42,209] [INFO] Task started: Blastn
[2023-06-19 03:53:42,209] [INFO] Running command: blastn -query GCA_018239665.1_ASM1823966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga24adcd8-1d46-4581-970a-d0adf69b64ef/dqc_reference/reference_markers.fasta -out GCA_018239665.1_ASM1823966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:53:42,870] [INFO] Task succeeded: Blastn
[2023-06-19 03:53:42,874] [INFO] Selected 24 target genomes.
[2023-06-19 03:53:42,875] [INFO] Target genome list was writen to GCA_018239665.1_ASM1823966v1_genomic.fna/target_genomes.txt
[2023-06-19 03:53:42,905] [INFO] Task started: fastANI
[2023-06-19 03:53:42,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg317d5c4b-6fd3-4851-9c65-fa83f9c090cf/GCA_018239665.1_ASM1823966v1_genomic.fna.gz --refList GCA_018239665.1_ASM1823966v1_genomic.fna/target_genomes.txt --output GCA_018239665.1_ASM1823966v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:53:57,101] [INFO] Task succeeded: fastANI
[2023-06-19 03:53:57,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga24adcd8-1d46-4581-970a-d0adf69b64ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:53:57,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga24adcd8-1d46-4581-970a-d0adf69b64ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:53:57,103] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:53:57,104] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 03:53:57,104] [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
--------------------------------------------------------------------------------
[2023-06-19 03:53:57,105] [INFO] DFAST Taxonomy check result was written to GCA_018239665.1_ASM1823966v1_genomic.fna/tc_result.tsv
[2023-06-19 03:53:57,106] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:53:57,106] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:53:57,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga24adcd8-1d46-4581-970a-d0adf69b64ef/dqc_reference/checkm_data
[2023-06-19 03:53:57,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:53:57,138] [INFO] Task started: CheckM
[2023-06-19 03:53:57,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018239665.1_ASM1823966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018239665.1_ASM1823966v1_genomic.fna/checkm_input GCA_018239665.1_ASM1823966v1_genomic.fna/checkm_result
[2023-06-19 03:54:22,183] [INFO] Task succeeded: CheckM
[2023-06-19 03:54:22,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:54:22,211] [INFO] ===== Completeness check finished =====
[2023-06-19 03:54:22,212] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:54:22,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018239665.1_ASM1823966v1_genomic.fna/markers.fasta)
[2023-06-19 03:54:22,212] [INFO] Task started: Blastn
[2023-06-19 03:54:22,213] [INFO] Running command: blastn -query GCA_018239665.1_ASM1823966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga24adcd8-1d46-4581-970a-d0adf69b64ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_018239665.1_ASM1823966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:54:23,281] [INFO] Task succeeded: Blastn
[2023-06-19 03:54:23,286] [INFO] Selected 12 target genomes.
[2023-06-19 03:54:23,287] [INFO] Target genome list was writen to GCA_018239665.1_ASM1823966v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:54:23,293] [INFO] Task started: fastANI
[2023-06-19 03:54:23,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg317d5c4b-6fd3-4851-9c65-fa83f9c090cf/GCA_018239665.1_ASM1823966v1_genomic.fna.gz --refList GCA_018239665.1_ASM1823966v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018239665.1_ASM1823966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:54:27,911] [INFO] Task succeeded: fastANI
[2023-06-19 03:54:27,920] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:54:27,921] [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_018239665.1	s__SZAS-10 sp018239665	100.0	730	742	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Rhabdochlamydiaceae;g__SZAS-10	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018240225.1	s__SZAS-10 sp018240225	81.9822	479	742	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Rhabdochlamydiaceae;g__SZAS-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239725.1	s__SZAS-10 sp018239725	81.7647	463	742	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Rhabdochlamydiaceae;g__SZAS-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240065.1	s__CAJCHM01 sp018240065	76.434	91	742	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Rhabdochlamydiaceae;g__CAJCHM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:54:27,923] [INFO] GTDB search result was written to GCA_018239665.1_ASM1823966v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:54:27,923] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:54:27,926] [INFO] DFAST_QC result json was written to GCA_018239665.1_ASM1823966v1_genomic.fna/dqc_result.json
[2023-06-19 03:54:27,926] [INFO] DFAST_QC completed!
[2023-06-19 03:54:27,926] [INFO] Total running time: 0h0m54s