[2023-06-13 10:10:44,214] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:44,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:44,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg2403aacc-65fc-4c22-badb-44ed4715cba8/dqc_reference
[2023-06-13 10:10:47,163] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:10:47,165] [INFO] Task started: Prodigal
[2023-06-13 10:10:47,166] [INFO] Running command: gunzip -c /var/lib/cwl/stgd43d8e83-82ad-40e3-9f86-ed6d85e81b91/GCA_022704345.1_ASM2270434v1_genomic.fna.gz | prodigal -d GCA_022704345.1_ASM2270434v1_genomic.fna/cds.fna -a GCA_022704345.1_ASM2270434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:10:53,609] [INFO] Task succeeded: Prodigal
[2023-06-13 10:10:53,609] [INFO] Task started: HMMsearch
[2023-06-13 10:10:53,610] [INFO] Running command: hmmsearch --tblout GCA_022704345.1_ASM2270434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2403aacc-65fc-4c22-badb-44ed4715cba8/dqc_reference/reference_markers.hmm GCA_022704345.1_ASM2270434v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:10:53,882] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:10:53,884] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd43d8e83-82ad-40e3-9f86-ed6d85e81b91/GCA_022704345.1_ASM2270434v1_genomic.fna.gz]
[2023-06-13 10:10:53,919] [INFO] Query marker FASTA was written to GCA_022704345.1_ASM2270434v1_genomic.fna/markers.fasta
[2023-06-13 10:10:53,919] [INFO] Task started: Blastn
[2023-06-13 10:10:53,919] [INFO] Running command: blastn -query GCA_022704345.1_ASM2270434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2403aacc-65fc-4c22-badb-44ed4715cba8/dqc_reference/reference_markers.fasta -out GCA_022704345.1_ASM2270434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:10:54,552] [INFO] Task succeeded: Blastn
[2023-06-13 10:10:54,566] [INFO] Selected 6 target genomes.
[2023-06-13 10:10:54,567] [INFO] Target genome list was writen to GCA_022704345.1_ASM2270434v1_genomic.fna/target_genomes.txt
[2023-06-13 10:10:54,570] [INFO] Task started: fastANI
[2023-06-13 10:10:54,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43d8e83-82ad-40e3-9f86-ed6d85e81b91/GCA_022704345.1_ASM2270434v1_genomic.fna.gz --refList GCA_022704345.1_ASM2270434v1_genomic.fna/target_genomes.txt --output GCA_022704345.1_ASM2270434v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:02,192] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:02,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2403aacc-65fc-4c22-badb-44ed4715cba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:02,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2403aacc-65fc-4c22-badb-44ed4715cba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:02,194] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:02,194] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:11:02,194] [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 10:11:02,196] [INFO] DFAST Taxonomy check result was written to GCA_022704345.1_ASM2270434v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:02,196] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:02,197] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:02,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2403aacc-65fc-4c22-badb-44ed4715cba8/dqc_reference/checkm_data
[2023-06-13 10:11:02,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:02,232] [INFO] Task started: CheckM
[2023-06-13 10:11:02,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022704345.1_ASM2270434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022704345.1_ASM2270434v1_genomic.fna/checkm_input GCA_022704345.1_ASM2270434v1_genomic.fna/checkm_result
[2023-06-13 10:11:28,525] [INFO] Task succeeded: CheckM
[2023-06-13 10:11:28,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.24%
Strain heterogeneity: 37.50%
--------------------------------------------------------------------------------
[2023-06-13 10:11:28,556] [INFO] ===== Completeness check finished =====
[2023-06-13 10:11:28,556] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:11:28,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022704345.1_ASM2270434v1_genomic.fna/markers.fasta)
[2023-06-13 10:11:28,557] [INFO] Task started: Blastn
[2023-06-13 10:11:28,557] [INFO] Running command: blastn -query GCA_022704345.1_ASM2270434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2403aacc-65fc-4c22-badb-44ed4715cba8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022704345.1_ASM2270434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:29,374] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:29,379] [INFO] Selected 12 target genomes.
[2023-06-13 10:11:29,379] [INFO] Target genome list was writen to GCA_022704345.1_ASM2270434v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:11:29,388] [INFO] Task started: fastANI
[2023-06-13 10:11:29,388] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43d8e83-82ad-40e3-9f86-ed6d85e81b91/GCA_022704345.1_ASM2270434v1_genomic.fna.gz --refList GCA_022704345.1_ASM2270434v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022704345.1_ASM2270434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:11:36,683] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:36,690] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:11:36,690] [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_002071085.1	s__MWEM01 sp002071085	99.9443	736	782	d__Bacteria;p__Thermotogota;c__Thermotogae;o__MWEM01;f__MWEM01;g__MWEM01	95.0	99.70	99.68	0.94	0.92	3	conclusive
GCA_012744415.1	s__MWEM01 sp012744415	78.8414	315	782	d__Bacteria;p__Thermotogota;c__Thermotogae;o__MWEM01;f__MWEM01;g__MWEM01	95.0	99.12	99.12	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-13 10:11:36,692] [INFO] GTDB search result was written to GCA_022704345.1_ASM2270434v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:11:36,693] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:11:36,695] [INFO] DFAST_QC result json was written to GCA_022704345.1_ASM2270434v1_genomic.fna/dqc_result.json
[2023-06-13 10:11:36,695] [INFO] DFAST_QC completed!
[2023-06-13 10:11:36,696] [INFO] Total running time: 0h0m52s