[2023-06-19 09:00:06,793] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:00:06,795] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:00:06,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d55d204-2e9d-4313-89ea-ecaa357740d2/dqc_reference
[2023-06-19 09:00:08,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:00:08,089] [INFO] Task started: Prodigal
[2023-06-19 09:00:08,090] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dde0501-a83a-4a3c-8403-29bf07592b24/GCA_018240135.1_ASM1824013v1_genomic.fna.gz | prodigal -d GCA_018240135.1_ASM1824013v1_genomic.fna/cds.fna -a GCA_018240135.1_ASM1824013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:00:12,293] [INFO] Task succeeded: Prodigal
[2023-06-19 09:00:12,294] [INFO] Task started: HMMsearch
[2023-06-19 09:00:12,294] [INFO] Running command: hmmsearch --tblout GCA_018240135.1_ASM1824013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d55d204-2e9d-4313-89ea-ecaa357740d2/dqc_reference/reference_markers.hmm GCA_018240135.1_ASM1824013v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:00:12,524] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:00:12,525] [INFO] Found 6/6 markers.
[2023-06-19 09:00:12,546] [INFO] Query marker FASTA was written to GCA_018240135.1_ASM1824013v1_genomic.fna/markers.fasta
[2023-06-19 09:00:12,547] [INFO] Task started: Blastn
[2023-06-19 09:00:12,547] [INFO] Running command: blastn -query GCA_018240135.1_ASM1824013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d55d204-2e9d-4313-89ea-ecaa357740d2/dqc_reference/reference_markers.fasta -out GCA_018240135.1_ASM1824013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:00:13,188] [INFO] Task succeeded: Blastn
[2023-06-19 09:00:13,193] [INFO] Selected 15 target genomes.
[2023-06-19 09:00:13,195] [INFO] Target genome list was writen to GCA_018240135.1_ASM1824013v1_genomic.fna/target_genomes.txt
[2023-06-19 09:00:13,198] [INFO] Task started: fastANI
[2023-06-19 09:00:13,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dde0501-a83a-4a3c-8403-29bf07592b24/GCA_018240135.1_ASM1824013v1_genomic.fna.gz --refList GCA_018240135.1_ASM1824013v1_genomic.fna/target_genomes.txt --output GCA_018240135.1_ASM1824013v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:00:24,417] [INFO] Task succeeded: fastANI
[2023-06-19 09:00:24,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d55d204-2e9d-4313-89ea-ecaa357740d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:00:24,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d55d204-2e9d-4313-89ea-ecaa357740d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:00:24,421] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:00:24,422] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 09:00:24,422] [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 09:00:24,426] [INFO] DFAST Taxonomy check result was written to GCA_018240135.1_ASM1824013v1_genomic.fna/tc_result.tsv
[2023-06-19 09:00:24,427] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:00:24,427] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:00:24,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d55d204-2e9d-4313-89ea-ecaa357740d2/dqc_reference/checkm_data
[2023-06-19 09:00:24,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:00:24,454] [INFO] Task started: CheckM
[2023-06-19 09:00:24,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018240135.1_ASM1824013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018240135.1_ASM1824013v1_genomic.fna/checkm_input GCA_018240135.1_ASM1824013v1_genomic.fna/checkm_result
[2023-06-19 09:00:44,765] [INFO] Task succeeded: CheckM
[2023-06-19 09:00:44,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:00:44,797] [INFO] ===== Completeness check finished =====
[2023-06-19 09:00:44,797] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:00:44,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018240135.1_ASM1824013v1_genomic.fna/markers.fasta)
[2023-06-19 09:00:44,798] [INFO] Task started: Blastn
[2023-06-19 09:00:44,798] [INFO] Running command: blastn -query GCA_018240135.1_ASM1824013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d55d204-2e9d-4313-89ea-ecaa357740d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018240135.1_ASM1824013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:00:45,775] [INFO] Task succeeded: Blastn
[2023-06-19 09:00:45,781] [INFO] Selected 21 target genomes.
[2023-06-19 09:00:45,782] [INFO] Target genome list was writen to GCA_018240135.1_ASM1824013v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:00:45,793] [INFO] Task started: fastANI
[2023-06-19 09:00:45,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dde0501-a83a-4a3c-8403-29bf07592b24/GCA_018240135.1_ASM1824013v1_genomic.fna.gz --refList GCA_018240135.1_ASM1824013v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018240135.1_ASM1824013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:00:53,243] [INFO] Task succeeded: fastANI
[2023-06-19 09:00:53,251] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:00:53,252] [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_018240135.1	s__SZAS-13 sp018240135	100.0	529	531	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Rhabdochlamydiaceae;g__SZAS-13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018240065.1	s__CAJCHM01 sp018240065	76.7103	61	531	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Rhabdochlamydiaceae;g__CAJCHM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970255.1	s__CAJCHM01 sp903970255	76.2667	53	531	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 09:00:53,255] [INFO] GTDB search result was written to GCA_018240135.1_ASM1824013v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:00:53,256] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:00:53,261] [INFO] DFAST_QC result json was written to GCA_018240135.1_ASM1824013v1_genomic.fna/dqc_result.json
[2023-06-19 09:00:53,261] [INFO] DFAST_QC completed!
[2023-06-19 09:00:53,262] [INFO] Total running time: 0h0m46s