[2023-06-19 05:38:04,975] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:38:04,977] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:38:04,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg146f7a54-214e-4e76-93da-9447479bbfdb/dqc_reference
[2023-06-19 05:38:06,328] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:38:06,329] [INFO] Task started: Prodigal
[2023-06-19 05:38:06,329] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd535f51-ce1a-4783-b343-4cb0e1d1164c/GCA_018399055.1_ASM1839905v1_genomic.fna.gz | prodigal -d GCA_018399055.1_ASM1839905v1_genomic.fna/cds.fna -a GCA_018399055.1_ASM1839905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:38:11,378] [INFO] Task succeeded: Prodigal
[2023-06-19 05:38:11,378] [INFO] Task started: HMMsearch
[2023-06-19 05:38:11,378] [INFO] Running command: hmmsearch --tblout GCA_018399055.1_ASM1839905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg146f7a54-214e-4e76-93da-9447479bbfdb/dqc_reference/reference_markers.hmm GCA_018399055.1_ASM1839905v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:38:11,565] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:38:11,566] [INFO] Found 6/6 markers.
[2023-06-19 05:38:11,596] [INFO] Query marker FASTA was written to GCA_018399055.1_ASM1839905v1_genomic.fna/markers.fasta
[2023-06-19 05:38:11,596] [INFO] Task started: Blastn
[2023-06-19 05:38:11,596] [INFO] Running command: blastn -query GCA_018399055.1_ASM1839905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg146f7a54-214e-4e76-93da-9447479bbfdb/dqc_reference/reference_markers.fasta -out GCA_018399055.1_ASM1839905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:38:12,136] [INFO] Task succeeded: Blastn
[2023-06-19 05:38:12,139] [INFO] Selected 15 target genomes.
[2023-06-19 05:38:12,140] [INFO] Target genome list was writen to GCA_018399055.1_ASM1839905v1_genomic.fna/target_genomes.txt
[2023-06-19 05:38:12,141] [INFO] Task started: fastANI
[2023-06-19 05:38:12,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd535f51-ce1a-4783-b343-4cb0e1d1164c/GCA_018399055.1_ASM1839905v1_genomic.fna.gz --refList GCA_018399055.1_ASM1839905v1_genomic.fna/target_genomes.txt --output GCA_018399055.1_ASM1839905v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:38:20,185] [INFO] Task succeeded: fastANI
[2023-06-19 05:38:20,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg146f7a54-214e-4e76-93da-9447479bbfdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:38:20,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg146f7a54-214e-4e76-93da-9447479bbfdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:38:20,187] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:38:20,187] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:38:20,187] [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 05:38:20,189] [INFO] DFAST Taxonomy check result was written to GCA_018399055.1_ASM1839905v1_genomic.fna/tc_result.tsv
[2023-06-19 05:38:20,190] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:38:20,190] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:38:20,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg146f7a54-214e-4e76-93da-9447479bbfdb/dqc_reference/checkm_data
[2023-06-19 05:38:20,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:38:20,216] [INFO] Task started: CheckM
[2023-06-19 05:38:20,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018399055.1_ASM1839905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018399055.1_ASM1839905v1_genomic.fna/checkm_input GCA_018399055.1_ASM1839905v1_genomic.fna/checkm_result
[2023-06-19 05:38:41,358] [INFO] Task succeeded: CheckM
[2023-06-19 05:38:41,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:38:41,384] [INFO] ===== Completeness check finished =====
[2023-06-19 05:38:41,384] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:38:41,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018399055.1_ASM1839905v1_genomic.fna/markers.fasta)
[2023-06-19 05:38:41,385] [INFO] Task started: Blastn
[2023-06-19 05:38:41,385] [INFO] Running command: blastn -query GCA_018399055.1_ASM1839905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg146f7a54-214e-4e76-93da-9447479bbfdb/dqc_reference/reference_markers_gtdb.fasta -out GCA_018399055.1_ASM1839905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:38:42,153] [INFO] Task succeeded: Blastn
[2023-06-19 05:38:42,158] [INFO] Selected 20 target genomes.
[2023-06-19 05:38:42,158] [INFO] Target genome list was writen to GCA_018399055.1_ASM1839905v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:38:42,204] [INFO] Task started: fastANI
[2023-06-19 05:38:42,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd535f51-ce1a-4783-b343-4cb0e1d1164c/GCA_018399055.1_ASM1839905v1_genomic.fna.gz --refList GCA_018399055.1_ASM1839905v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018399055.1_ASM1839905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:38:49,213] [INFO] Task succeeded: fastANI
[2023-06-19 05:38:49,217] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:38:49,217] [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_018399055.1	s__Neptunochlamydia sp018399055	100.0	714	714	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Simkaniaceae;g__Neptunochlamydia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018399075.1	s__Neptunochlamydia sp018399075	77.4186	122	714	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Simkaniaceae;g__Neptunochlamydia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356785.1	s__Neptunochlamydia vexilliferae	77.3173	67	714	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Simkaniaceae;g__Neptunochlamydia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 05:38:49,219] [INFO] GTDB search result was written to GCA_018399055.1_ASM1839905v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:38:49,220] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:38:49,222] [INFO] DFAST_QC result json was written to GCA_018399055.1_ASM1839905v1_genomic.fna/dqc_result.json
[2023-06-19 05:38:49,222] [INFO] DFAST_QC completed!
[2023-06-19 05:38:49,223] [INFO] Total running time: 0h0m44s