[2023-06-08 16:39:11,101] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:39:11,103] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:39:11,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a890684-c65d-4639-a489-2bd2a25f674e/dqc_reference
[2023-06-08 16:39:12,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:39:12,330] [INFO] Task started: Prodigal
[2023-06-08 16:39:12,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e05d5c6-c5e6-4cb6-9114-6ab9e887d873/GCA_945886445.1_ME-08apr19-267_genomic.fna.gz | prodigal -d GCA_945886445.1_ME-08apr19-267_genomic.fna/cds.fna -a GCA_945886445.1_ME-08apr19-267_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:39:19,318] [INFO] Task succeeded: Prodigal
[2023-06-08 16:39:19,318] [INFO] Task started: HMMsearch
[2023-06-08 16:39:19,319] [INFO] Running command: hmmsearch --tblout GCA_945886445.1_ME-08apr19-267_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a890684-c65d-4639-a489-2bd2a25f674e/dqc_reference/reference_markers.hmm GCA_945886445.1_ME-08apr19-267_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:39:19,548] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:39:19,550] [INFO] Found 6/6 markers.
[2023-06-08 16:39:19,580] [INFO] Query marker FASTA was written to GCA_945886445.1_ME-08apr19-267_genomic.fna/markers.fasta
[2023-06-08 16:39:19,580] [INFO] Task started: Blastn
[2023-06-08 16:39:19,581] [INFO] Running command: blastn -query GCA_945886445.1_ME-08apr19-267_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a890684-c65d-4639-a489-2bd2a25f674e/dqc_reference/reference_markers.fasta -out GCA_945886445.1_ME-08apr19-267_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:39:20,156] [INFO] Task succeeded: Blastn
[2023-06-08 16:39:20,560] [INFO] Selected 15 target genomes.
[2023-06-08 16:39:20,561] [INFO] Target genome list was writen to GCA_945886445.1_ME-08apr19-267_genomic.fna/target_genomes.txt
[2023-06-08 16:39:20,565] [INFO] Task started: fastANI
[2023-06-08 16:39:20,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e05d5c6-c5e6-4cb6-9114-6ab9e887d873/GCA_945886445.1_ME-08apr19-267_genomic.fna.gz --refList GCA_945886445.1_ME-08apr19-267_genomic.fna/target_genomes.txt --output GCA_945886445.1_ME-08apr19-267_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:39:27,389] [INFO] Task succeeded: fastANI
[2023-06-08 16:39:27,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a890684-c65d-4639-a489-2bd2a25f674e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:39:27,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a890684-c65d-4639-a489-2bd2a25f674e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:39:27,392] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:39:27,392] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 16:39:27,393] [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
--------------------------------------------------------------------------------
[2023-06-08 16:39:27,395] [INFO] DFAST Taxonomy check result was written to GCA_945886445.1_ME-08apr19-267_genomic.fna/tc_result.tsv
[2023-06-08 16:39:27,396] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:39:27,396] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:39:27,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a890684-c65d-4639-a489-2bd2a25f674e/dqc_reference/checkm_data
[2023-06-08 16:39:27,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:39:27,433] [INFO] Task started: CheckM
[2023-06-08 16:39:27,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945886445.1_ME-08apr19-267_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945886445.1_ME-08apr19-267_genomic.fna/checkm_input GCA_945886445.1_ME-08apr19-267_genomic.fna/checkm_result
[2023-06-08 16:39:54,853] [INFO] Task succeeded: CheckM
[2023-06-08 16:39:54,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:39:54,881] [INFO] ===== Completeness check finished =====
[2023-06-08 16:39:54,882] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:39:54,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945886445.1_ME-08apr19-267_genomic.fna/markers.fasta)
[2023-06-08 16:39:54,883] [INFO] Task started: Blastn
[2023-06-08 16:39:54,883] [INFO] Running command: blastn -query GCA_945886445.1_ME-08apr19-267_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a890684-c65d-4639-a489-2bd2a25f674e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945886445.1_ME-08apr19-267_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:39:55,686] [INFO] Task succeeded: Blastn
[2023-06-08 16:39:55,691] [INFO] Selected 18 target genomes.
[2023-06-08 16:39:55,691] [INFO] Target genome list was writen to GCA_945886445.1_ME-08apr19-267_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:39:55,700] [INFO] Task started: fastANI
[2023-06-08 16:39:55,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e05d5c6-c5e6-4cb6-9114-6ab9e887d873/GCA_945886445.1_ME-08apr19-267_genomic.fna.gz --refList GCA_945886445.1_ME-08apr19-267_genomic.fna/target_genomes_gtdb.txt --output GCA_945886445.1_ME-08apr19-267_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:40:01,306] [INFO] Task succeeded: fastANI
[2023-06-08 16:40:01,317] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 16:40:01,318] [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_013205145.1	s__F1-20-MAGs119 sp013205145	91.799	432	666	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	96.62	96.62	0.79	0.79	2	-
GCA_903858075.1	s__F1-20-MAGs119 sp903858075	91.1791	369	666	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711295.1	s__F1-20-MAGs119 sp009711295	86.3243	471	666	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	98.43	97.32	0.85	0.80	3	-
GCA_903904615.1	s__UBA2093 sp903904615	78.0918	51	666	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970175.1	s__F1-20-MAGs119 sp018970175	76.7594	59	666	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703055.1	s__UBA2093 sp009703055	75.8402	50	666	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 16:40:01,320] [INFO] GTDB search result was written to GCA_945886445.1_ME-08apr19-267_genomic.fna/result_gtdb.tsv
[2023-06-08 16:40:01,321] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:40:01,324] [INFO] DFAST_QC result json was written to GCA_945886445.1_ME-08apr19-267_genomic.fna/dqc_result.json
[2023-06-08 16:40:01,324] [INFO] DFAST_QC completed!
[2023-06-08 16:40:01,324] [INFO] Total running time: 0h0m50s