[2023-06-18 22:57:18,302] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:57:18,305] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:57:18,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b8601b1-5968-4c02-b7e2-a00f2f3e1fa1/dqc_reference
[2023-06-18 22:57:19,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:57:19,567] [INFO] Task started: Prodigal
[2023-06-18 22:57:19,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg44d0dcef-c746-4d05-aea6-70064fca7c41/GCA_014869295.1_ASM1486929v1_genomic.fna.gz | prodigal -d GCA_014869295.1_ASM1486929v1_genomic.fna/cds.fna -a GCA_014869295.1_ASM1486929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:57:24,256] [INFO] Task succeeded: Prodigal
[2023-06-18 22:57:24,256] [INFO] Task started: HMMsearch
[2023-06-18 22:57:24,257] [INFO] Running command: hmmsearch --tblout GCA_014869295.1_ASM1486929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b8601b1-5968-4c02-b7e2-a00f2f3e1fa1/dqc_reference/reference_markers.hmm GCA_014869295.1_ASM1486929v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:57:24,486] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:57:24,488] [INFO] Found 6/6 markers.
[2023-06-18 22:57:24,513] [INFO] Query marker FASTA was written to GCA_014869295.1_ASM1486929v1_genomic.fna/markers.fasta
[2023-06-18 22:57:24,514] [INFO] Task started: Blastn
[2023-06-18 22:57:24,514] [INFO] Running command: blastn -query GCA_014869295.1_ASM1486929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b8601b1-5968-4c02-b7e2-a00f2f3e1fa1/dqc_reference/reference_markers.fasta -out GCA_014869295.1_ASM1486929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:25,184] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:25,188] [INFO] Selected 21 target genomes.
[2023-06-18 22:57:25,188] [INFO] Target genome list was writen to GCA_014869295.1_ASM1486929v1_genomic.fna/target_genomes.txt
[2023-06-18 22:57:25,191] [INFO] Task started: fastANI
[2023-06-18 22:57:25,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg44d0dcef-c746-4d05-aea6-70064fca7c41/GCA_014869295.1_ASM1486929v1_genomic.fna.gz --refList GCA_014869295.1_ASM1486929v1_genomic.fna/target_genomes.txt --output GCA_014869295.1_ASM1486929v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:35,858] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:35,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b8601b1-5968-4c02-b7e2-a00f2f3e1fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:35,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b8601b1-5968-4c02-b7e2-a00f2f3e1fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:35,861] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:35,861] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:57:35,861] [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
--------------------------------------------------------------------------------
[2023-06-18 22:57:35,864] [INFO] DFAST Taxonomy check result was written to GCA_014869295.1_ASM1486929v1_genomic.fna/tc_result.tsv
[2023-06-18 22:57:35,864] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:35,865] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:35,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b8601b1-5968-4c02-b7e2-a00f2f3e1fa1/dqc_reference/checkm_data
[2023-06-18 22:57:35,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:35,891] [INFO] Task started: CheckM
[2023-06-18 22:57:35,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014869295.1_ASM1486929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014869295.1_ASM1486929v1_genomic.fna/checkm_input GCA_014869295.1_ASM1486929v1_genomic.fna/checkm_result
[2023-06-18 22:57:57,100] [INFO] Task succeeded: CheckM
[2023-06-18 22:57:57,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:57:57,122] [INFO] ===== Completeness check finished =====
[2023-06-18 22:57:57,123] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:57:57,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014869295.1_ASM1486929v1_genomic.fna/markers.fasta)
[2023-06-18 22:57:57,123] [INFO] Task started: Blastn
[2023-06-18 22:57:57,124] [INFO] Running command: blastn -query GCA_014869295.1_ASM1486929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b8601b1-5968-4c02-b7e2-a00f2f3e1fa1/dqc_reference/reference_markers_gtdb.fasta -out GCA_014869295.1_ASM1486929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:58,290] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:58,294] [INFO] Selected 8 target genomes.
[2023-06-18 22:57:58,294] [INFO] Target genome list was writen to GCA_014869295.1_ASM1486929v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:57:58,297] [INFO] Task started: fastANI
[2023-06-18 22:57:58,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg44d0dcef-c746-4d05-aea6-70064fca7c41/GCA_014869295.1_ASM1486929v1_genomic.fna.gz --refList GCA_014869295.1_ASM1486929v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014869295.1_ASM1486929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:58:02,285] [INFO] Task succeeded: fastANI
[2023-06-18 22:58:02,298] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:58:02,298] [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_001916715.1	s__F23-B02 sp001916715	97.9898	543	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.22	97.52	0.91	0.88	7	conclusive
GCA_002472405.1	s__F23-B02 sp002472405	94.8573	496	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.11	97.78	0.86	0.83	6	-
GCA_004558025.1	s__F23-B02 sp004558025	85.0201	416	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	99.18	99.18	0.86	0.86	2	-
GCA_900545805.1	s__F23-B02 sp900545805	84.3651	390	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	99.34	98.77	0.94	0.94	3	-
GCA_004553495.1	s__F23-B02 sp004553495	82.1342	315	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.58	98.56	0.81	0.81	3	-
GCA_900772725.1	s__F23-B02 sp900772725	81.4529	248	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760205.1	s__F23-B02 sp900760205	80.5275	227	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.80	98.80	0.91	0.91	2	-
GCA_016292445.1	s__F23-B02 sp016292445	79.6589	185	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	97.48	96.04	0.83	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-18 22:58:02,300] [INFO] GTDB search result was written to GCA_014869295.1_ASM1486929v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:58:02,301] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:58:02,304] [INFO] DFAST_QC result json was written to GCA_014869295.1_ASM1486929v1_genomic.fna/dqc_result.json
[2023-06-18 22:58:02,304] [INFO] DFAST_QC completed!
[2023-06-18 22:58:02,304] [INFO] Total running time: 0h0m44s