[2023-06-30 18:03:44,004] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:03:44,006] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:03:44,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg64c3a0d7-c1d5-4619-89fe-708318270075/dqc_reference
[2023-06-30 18:03:46,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:03:46,566] [INFO] Task started: Prodigal
[2023-06-30 18:03:46,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg50b7c97a-313a-4263-838f-97f904020110/GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna.gz | prodigal -d GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/cds.fna -a GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:03:50,477] [INFO] Task succeeded: Prodigal
[2023-06-30 18:03:50,478] [INFO] Task started: HMMsearch
[2023-06-30 18:03:50,478] [INFO] Running command: hmmsearch --tblout GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64c3a0d7-c1d5-4619-89fe-708318270075/dqc_reference/reference_markers.hmm GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:03:50,656] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:03:50,657] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg50b7c97a-313a-4263-838f-97f904020110/GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna.gz]
[2023-06-30 18:03:50,679] [INFO] Query marker FASTA was written to GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/markers.fasta
[2023-06-30 18:03:50,680] [INFO] Task started: Blastn
[2023-06-30 18:03:50,680] [INFO] Running command: blastn -query GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/markers.fasta -db /var/lib/cwl/stg64c3a0d7-c1d5-4619-89fe-708318270075/dqc_reference/reference_markers.fasta -out GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:03:51,541] [INFO] Task succeeded: Blastn
[2023-06-30 18:03:51,546] [INFO] Selected 14 target genomes.
[2023-06-30 18:03:51,547] [INFO] Target genome list was writen to GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/target_genomes.txt
[2023-06-30 18:03:51,550] [INFO] Task started: fastANI
[2023-06-30 18:03:51,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b7c97a-313a-4263-838f-97f904020110/GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna.gz --refList GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/target_genomes.txt --output GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:04:00,595] [INFO] Task succeeded: fastANI
[2023-06-30 18:04:00,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64c3a0d7-c1d5-4619-89fe-708318270075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:04:00,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64c3a0d7-c1d5-4619-89fe-708318270075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:04:00,598] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:04:00,599] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 18:04:00,599] [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
--------------------------------------------------------------------------------
[2023-06-30 18:04:00,602] [INFO] DFAST Taxonomy check result was written to GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/tc_result.tsv
[2023-06-30 18:04:00,602] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:04:00,603] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:04:00,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64c3a0d7-c1d5-4619-89fe-708318270075/dqc_reference/checkm_data
[2023-06-30 18:04:00,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:04:00,629] [INFO] Task started: CheckM
[2023-06-30 18:04:00,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/checkm_input GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/checkm_result
[2023-06-30 18:04:19,161] [INFO] Task succeeded: CheckM
[2023-06-30 18:04:19,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:04:19,183] [INFO] ===== Completeness check finished =====
[2023-06-30 18:04:19,184] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:04:19,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/markers.fasta)
[2023-06-30 18:04:19,184] [INFO] Task started: Blastn
[2023-06-30 18:04:19,184] [INFO] Running command: blastn -query GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/markers.fasta -db /var/lib/cwl/stg64c3a0d7-c1d5-4619-89fe-708318270075/dqc_reference/reference_markers_gtdb.fasta -out GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:04:20,026] [INFO] Task succeeded: Blastn
[2023-06-30 18:04:20,031] [INFO] Selected 11 target genomes.
[2023-06-30 18:04:20,031] [INFO] Target genome list was writen to GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:04:20,037] [INFO] Task started: fastANI
[2023-06-30 18:04:20,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b7c97a-313a-4263-838f-97f904020110/GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna.gz --refList GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/target_genomes_gtdb.txt --output GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:04:24,302] [INFO] Task succeeded: fastANI
[2023-06-30 18:04:24,309] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:04:24,309] [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_903870905.1	s__CAIQEU01 sp903870905	99.6806	189	208	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__CAIQEU01	95.0	99.73	99.45	0.95	0.89	17	conclusive
GCA_903847955.1	s__CAINFA01 sp903847955	77.0506	58	208	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__CAINFA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:04:24,312] [INFO] GTDB search result was written to GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/result_gtdb.tsv
[2023-06-30 18:04:24,312] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:04:24,314] [INFO] DFAST_QC result json was written to GCA_903841075.1_freshwater_MAG_---_VK3_bin-1519_genomic.fna/dqc_result.json
[2023-06-30 18:04:24,315] [INFO] DFAST_QC completed!
[2023-06-30 18:04:24,315] [INFO] Total running time: 0h0m40s