[2023-06-13 23:59:04,266] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:59:04,306] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:59:04,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg62093b59-9b53-4085-97cd-39f3bd4b3b3e/dqc_reference
[2023-06-13 23:59:05,553] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:59:05,554] [INFO] Task started: Prodigal
[2023-06-13 23:59:05,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg31d968ea-6199-488f-ac14-6aa264da8521/GCA_947488455.1_TH-Jun18-89_genomic.fna.gz | prodigal -d GCA_947488455.1_TH-Jun18-89_genomic.fna/cds.fna -a GCA_947488455.1_TH-Jun18-89_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:59:08,796] [INFO] Task succeeded: Prodigal
[2023-06-13 23:59:08,797] [INFO] Task started: HMMsearch
[2023-06-13 23:59:08,797] [INFO] Running command: hmmsearch --tblout GCA_947488455.1_TH-Jun18-89_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62093b59-9b53-4085-97cd-39f3bd4b3b3e/dqc_reference/reference_markers.hmm GCA_947488455.1_TH-Jun18-89_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:59:08,999] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:59:09,000] [INFO] Found 6/6 markers.
[2023-06-13 23:59:09,017] [INFO] Query marker FASTA was written to GCA_947488455.1_TH-Jun18-89_genomic.fna/markers.fasta
[2023-06-13 23:59:09,017] [INFO] Task started: Blastn
[2023-06-13 23:59:09,017] [INFO] Running command: blastn -query GCA_947488455.1_TH-Jun18-89_genomic.fna/markers.fasta -db /var/lib/cwl/stg62093b59-9b53-4085-97cd-39f3bd4b3b3e/dqc_reference/reference_markers.fasta -out GCA_947488455.1_TH-Jun18-89_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:59:09,596] [INFO] Task succeeded: Blastn
[2023-06-13 23:59:09,601] [INFO] Selected 12 target genomes.
[2023-06-13 23:59:09,602] [INFO] Target genome list was writen to GCA_947488455.1_TH-Jun18-89_genomic.fna/target_genomes.txt
[2023-06-13 23:59:09,605] [INFO] Task started: fastANI
[2023-06-13 23:59:09,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg31d968ea-6199-488f-ac14-6aa264da8521/GCA_947488455.1_TH-Jun18-89_genomic.fna.gz --refList GCA_947488455.1_TH-Jun18-89_genomic.fna/target_genomes.txt --output GCA_947488455.1_TH-Jun18-89_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:59:15,176] [INFO] Task succeeded: fastANI
[2023-06-13 23:59:15,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62093b59-9b53-4085-97cd-39f3bd4b3b3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:59:15,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62093b59-9b53-4085-97cd-39f3bd4b3b3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:59:15,179] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:59:15,179] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 23:59:15,179] [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 23:59:15,182] [INFO] DFAST Taxonomy check result was written to GCA_947488455.1_TH-Jun18-89_genomic.fna/tc_result.tsv
[2023-06-13 23:59:15,182] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:59:15,183] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:59:15,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62093b59-9b53-4085-97cd-39f3bd4b3b3e/dqc_reference/checkm_data
[2023-06-13 23:59:15,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:59:15,205] [INFO] Task started: CheckM
[2023-06-13 23:59:15,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947488455.1_TH-Jun18-89_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947488455.1_TH-Jun18-89_genomic.fna/checkm_input GCA_947488455.1_TH-Jun18-89_genomic.fna/checkm_result
[2023-06-13 23:59:32,423] [INFO] Task succeeded: CheckM
[2023-06-13 23:59:32,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:59:32,453] [INFO] ===== Completeness check finished =====
[2023-06-13 23:59:32,454] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:59:32,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947488455.1_TH-Jun18-89_genomic.fna/markers.fasta)
[2023-06-13 23:59:32,455] [INFO] Task started: Blastn
[2023-06-13 23:59:32,455] [INFO] Running command: blastn -query GCA_947488455.1_TH-Jun18-89_genomic.fna/markers.fasta -db /var/lib/cwl/stg62093b59-9b53-4085-97cd-39f3bd4b3b3e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947488455.1_TH-Jun18-89_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:59:33,283] [INFO] Task succeeded: Blastn
[2023-06-13 23:59:33,288] [INFO] Selected 16 target genomes.
[2023-06-13 23:59:33,288] [INFO] Target genome list was writen to GCA_947488455.1_TH-Jun18-89_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:59:33,300] [INFO] Task started: fastANI
[2023-06-13 23:59:33,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg31d968ea-6199-488f-ac14-6aa264da8521/GCA_947488455.1_TH-Jun18-89_genomic.fna.gz --refList GCA_947488455.1_TH-Jun18-89_genomic.fna/target_genomes_gtdb.txt --output GCA_947488455.1_TH-Jun18-89_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:59:38,096] [INFO] Task succeeded: fastANI
[2023-06-13 23:59:38,116] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 23:59:38,117] [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_005805045.1	s__BACL27 sp005805045	89.2055	185	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	99.25	99.23	0.81	0.81	3	-
GCA_002737635.1	s__BACL27 sp002737635	84.3148	146	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014190055.1	s__BACL27 sp014190055	80.3111	131	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	95.53	95.36	0.86	0.77	8	-
GCA_009923685.1	s__BACL27 sp009923685	79.6928	56	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009927565.1	s__BACL27 sp009927565	79.199	125	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462185.1	s__BACL27 sp016462185	78.9478	145	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	98.92	98.92	0.88	0.88	2	-
GCA_003569125.1	s__BACL27 sp003569125	78.5892	118	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014190295.1	s__BACL27 sp014190295	78.5565	137	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703975.1	s__BACL27 sp009703975	78.4433	87	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	97.18	96.93	0.73	0.69	4	-
GCA_016463105.1	s__BACL27 sp016463105	77.9904	104	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870935.1	s__BACL27 sp016870935	77.8344	113	326	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 23:59:38,120] [INFO] GTDB search result was written to GCA_947488455.1_TH-Jun18-89_genomic.fna/result_gtdb.tsv
[2023-06-13 23:59:38,120] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:59:38,124] [INFO] DFAST_QC result json was written to GCA_947488455.1_TH-Jun18-89_genomic.fna/dqc_result.json
[2023-06-13 23:59:38,124] [INFO] DFAST_QC completed!
[2023-06-13 23:59:38,124] [INFO] Total running time: 0h0m34s