[2023-06-29 12:58:21,683] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:58:21,703] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:58:21,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fb24f7b-8801-4601-888a-cae4c9289487/dqc_reference
[2023-06-29 12:58:22,892] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:58:22,893] [INFO] Task started: Prodigal
[2023-06-29 12:58:22,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ca6befb-01bd-418a-9022-aa332b397553/GCA_015075145.1_ASM1507514v1_genomic.fna.gz | prodigal -d GCA_015075145.1_ASM1507514v1_genomic.fna/cds.fna -a GCA_015075145.1_ASM1507514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:58:33,091] [INFO] Task succeeded: Prodigal
[2023-06-29 12:58:33,092] [INFO] Task started: HMMsearch
[2023-06-29 12:58:33,092] [INFO] Running command: hmmsearch --tblout GCA_015075145.1_ASM1507514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fb24f7b-8801-4601-888a-cae4c9289487/dqc_reference/reference_markers.hmm GCA_015075145.1_ASM1507514v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:58:33,305] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:58:33,306] [INFO] Found 6/6 markers.
[2023-06-29 12:58:33,338] [INFO] Query marker FASTA was written to GCA_015075145.1_ASM1507514v1_genomic.fna/markers.fasta
[2023-06-29 12:58:33,339] [INFO] Task started: Blastn
[2023-06-29 12:58:33,339] [INFO] Running command: blastn -query GCA_015075145.1_ASM1507514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fb24f7b-8801-4601-888a-cae4c9289487/dqc_reference/reference_markers.fasta -out GCA_015075145.1_ASM1507514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:58:33,910] [INFO] Task succeeded: Blastn
[2023-06-29 12:58:33,913] [INFO] Selected 10 target genomes.
[2023-06-29 12:58:33,914] [INFO] Target genome list was writen to GCA_015075145.1_ASM1507514v1_genomic.fna/target_genomes.txt
[2023-06-29 12:58:33,917] [INFO] Task started: fastANI
[2023-06-29 12:58:33,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca6befb-01bd-418a-9022-aa332b397553/GCA_015075145.1_ASM1507514v1_genomic.fna.gz --refList GCA_015075145.1_ASM1507514v1_genomic.fna/target_genomes.txt --output GCA_015075145.1_ASM1507514v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:58:38,972] [INFO] Task succeeded: fastANI
[2023-06-29 12:58:38,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fb24f7b-8801-4601-888a-cae4c9289487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:58:38,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fb24f7b-8801-4601-888a-cae4c9289487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:58:38,975] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:58:38,975] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:58:38,975] [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
--------------------------------------------------------------------------------
[2023-06-29 12:58:38,977] [INFO] DFAST Taxonomy check result was written to GCA_015075145.1_ASM1507514v1_genomic.fna/tc_result.tsv
[2023-06-29 12:58:38,977] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:58:38,978] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:58:38,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fb24f7b-8801-4601-888a-cae4c9289487/dqc_reference/checkm_data
[2023-06-29 12:58:38,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:58:39,024] [INFO] Task started: CheckM
[2023-06-29 12:58:39,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015075145.1_ASM1507514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015075145.1_ASM1507514v1_genomic.fna/checkm_input GCA_015075145.1_ASM1507514v1_genomic.fna/checkm_result
[2023-06-29 12:59:12,904] [INFO] Task succeeded: CheckM
[2023-06-29 12:59:12,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:59:12,923] [INFO] ===== Completeness check finished =====
[2023-06-29 12:59:12,924] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:59:12,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015075145.1_ASM1507514v1_genomic.fna/markers.fasta)
[2023-06-29 12:59:12,924] [INFO] Task started: Blastn
[2023-06-29 12:59:12,924] [INFO] Running command: blastn -query GCA_015075145.1_ASM1507514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fb24f7b-8801-4601-888a-cae4c9289487/dqc_reference/reference_markers_gtdb.fasta -out GCA_015075145.1_ASM1507514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:59:13,652] [INFO] Task succeeded: Blastn
[2023-06-29 12:59:13,656] [INFO] Selected 21 target genomes.
[2023-06-29 12:59:13,656] [INFO] Target genome list was writen to GCA_015075145.1_ASM1507514v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:59:13,668] [INFO] Task started: fastANI
[2023-06-29 12:59:13,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca6befb-01bd-418a-9022-aa332b397553/GCA_015075145.1_ASM1507514v1_genomic.fna.gz --refList GCA_015075145.1_ASM1507514v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015075145.1_ASM1507514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:59:27,890] [INFO] Task succeeded: fastANI
[2023-06-29 12:59:27,899] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:59:27,899] [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
GCF_900232105.1	s__Kuenenia stuttgartiensis	98.9855	1277	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Kuenenia	95.0	99.22	98.74	0.94	0.87	9	conclusive
GCA_016873165.1	s__Kuenenia sp016873165	79.2135	648	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Kuenenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525665.1	s__Brocadia sp011525665	78.4502	104	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873155.1	s__XYD2-FULL-41-16 sp016873155	78.3313	102	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__XYD2-FULL-41-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017347445.1	s__Brocadia pituitae	78.1526	150	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235875.1	s__XYD2-FULL-41-16 sp016235875	77.9055	76	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__XYD2-FULL-41-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360945.1	s__Brocadia sp013360945	77.2777	124	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830285.1	s__PLOWO2-12-38-17 sp001830285	77.0419	58	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__PLOWO2-12-38-17	95.0	95.07	95.07	0.84	0.84	2	-
GCA_001824485.1	s__2-12-FULL-39-13 sp001824485	77.0233	57	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__2-12-FULL-39-13	95.0	99.02	98.73	0.80	0.75	4	-
GCA_001828645.1	s__XYD2-FULL-41-16 sp001828645	76.2489	51	1441	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__XYD2-FULL-41-16	95.0	97.31	95.87	0.78	0.77	3	-
--------------------------------------------------------------------------------
[2023-06-29 12:59:27,901] [INFO] GTDB search result was written to GCA_015075145.1_ASM1507514v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:59:27,902] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:59:27,905] [INFO] DFAST_QC result json was written to GCA_015075145.1_ASM1507514v1_genomic.fna/dqc_result.json
[2023-06-29 12:59:27,905] [INFO] DFAST_QC completed!
[2023-06-29 12:59:27,905] [INFO] Total running time: 0h1m6s