[2023-06-04 19:38:04,129] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:38:04,132] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:38:04,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b57d6cf-2620-4036-a823-757489021c0b/dqc_reference
[2023-06-04 19:38:05,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:38:05,350] [INFO] Task started: Prodigal
[2023-06-04 19:38:05,350] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a5464c1-1d59-4256-831e-5e0ebe38324b/GCA_902617105.1_AG-919-M14_genomic.fna.gz | prodigal -d GCA_902617105.1_AG-919-M14_genomic.fna/cds.fna -a GCA_902617105.1_AG-919-M14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:11,660] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:11,660] [INFO] Task started: HMMsearch
[2023-06-04 19:38:11,661] [INFO] Running command: hmmsearch --tblout GCA_902617105.1_AG-919-M14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b57d6cf-2620-4036-a823-757489021c0b/dqc_reference/reference_markers.hmm GCA_902617105.1_AG-919-M14_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:11,820] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:11,822] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6a5464c1-1d59-4256-831e-5e0ebe38324b/GCA_902617105.1_AG-919-M14_genomic.fna.gz]
[2023-06-04 19:38:11,845] [INFO] Query marker FASTA was written to GCA_902617105.1_AG-919-M14_genomic.fna/markers.fasta
[2023-06-04 19:38:11,846] [INFO] Task started: Blastn
[2023-06-04 19:38:11,846] [INFO] Running command: blastn -query GCA_902617105.1_AG-919-M14_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b57d6cf-2620-4036-a823-757489021c0b/dqc_reference/reference_markers.fasta -out GCA_902617105.1_AG-919-M14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:12,419] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:12,425] [INFO] Selected 22 target genomes.
[2023-06-04 19:38:12,425] [INFO] Target genome list was writen to GCA_902617105.1_AG-919-M14_genomic.fna/target_genomes.txt
[2023-06-04 19:38:12,429] [INFO] Task started: fastANI
[2023-06-04 19:38:12,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a5464c1-1d59-4256-831e-5e0ebe38324b/GCA_902617105.1_AG-919-M14_genomic.fna.gz --refList GCA_902617105.1_AG-919-M14_genomic.fna/target_genomes.txt --output GCA_902617105.1_AG-919-M14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:24,276] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:24,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b57d6cf-2620-4036-a823-757489021c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:24,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b57d6cf-2620-4036-a823-757489021c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:24,278] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:38:24,278] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:38:24,278] [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
--------------------------------------------------------------------------------
[2023-06-04 19:38:24,280] [INFO] DFAST Taxonomy check result was written to GCA_902617105.1_AG-919-M14_genomic.fna/tc_result.tsv
[2023-06-04 19:38:24,281] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:24,281] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:24,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b57d6cf-2620-4036-a823-757489021c0b/dqc_reference/checkm_data
[2023-06-04 19:38:24,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:24,300] [INFO] Task started: CheckM
[2023-06-04 19:38:24,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902617105.1_AG-919-M14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902617105.1_AG-919-M14_genomic.fna/checkm_input GCA_902617105.1_AG-919-M14_genomic.fna/checkm_result
[2023-06-04 19:38:48,094] [INFO] Task succeeded: CheckM
[2023-06-04 19:38:48,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:38:48,115] [INFO] ===== Completeness check finished =====
[2023-06-04 19:38:48,115] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:38:48,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902617105.1_AG-919-M14_genomic.fna/markers.fasta)
[2023-06-04 19:38:48,116] [INFO] Task started: Blastn
[2023-06-04 19:38:48,116] [INFO] Running command: blastn -query GCA_902617105.1_AG-919-M14_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b57d6cf-2620-4036-a823-757489021c0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902617105.1_AG-919-M14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:48,871] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:48,875] [INFO] Selected 6 target genomes.
[2023-06-04 19:38:48,875] [INFO] Target genome list was writen to GCA_902617105.1_AG-919-M14_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:38:48,875] [INFO] Task started: fastANI
[2023-06-04 19:38:48,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a5464c1-1d59-4256-831e-5e0ebe38324b/GCA_902617105.1_AG-919-M14_genomic.fna.gz --refList GCA_902617105.1_AG-919-M14_genomic.fna/target_genomes_gtdb.txt --output GCA_902617105.1_AG-919-M14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:38:50,585] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:50,592] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:38:50,592] [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_002862705.1	s__UBA7446 sp002862705	98.3572	338	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	conclusive
GCA_002313325.1	s__UBA7446 sp002313325	93.044	225	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.90	99.90	0.92	0.92	2	-
GCA_009886265.1	s__UBA7446 sp009886265	90.7796	288	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862645.1	s__UBA7446 sp002862645	83.8681	290	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
GCA_002698745.1	s__UBA7446 sp002698745	83.5614	255	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478685.1	s__UBA7446 sp002478685	77.881	130	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.74	99.74	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-04 19:38:50,594] [INFO] GTDB search result was written to GCA_902617105.1_AG-919-M14_genomic.fna/result_gtdb.tsv
[2023-06-04 19:38:50,595] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:38:50,597] [INFO] DFAST_QC result json was written to GCA_902617105.1_AG-919-M14_genomic.fna/dqc_result.json
[2023-06-04 19:38:50,598] [INFO] DFAST_QC completed!
[2023-06-04 19:38:50,598] [INFO] Total running time: 0h0m46s