[2023-06-30 08:19:41,353] [INFO] DFAST_QC pipeline started.
[2023-06-30 08:19:41,355] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 08:19:41,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg85ca7018-79a9-46e4-ace4-4f1e4ce840ca/dqc_reference
[2023-06-30 08:19:44,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 08:19:44,239] [INFO] Task started: Prodigal
[2023-06-30 08:19:44,239] [INFO] Running command: gunzip -c /var/lib/cwl/stg12daa2bd-e005-4e7b-8091-7bf9ed9dbb05/GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna.gz | prodigal -d GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/cds.fna -a GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 08:19:46,621] [INFO] Task succeeded: Prodigal
[2023-06-30 08:19:46,621] [INFO] Task started: HMMsearch
[2023-06-30 08:19:46,621] [INFO] Running command: hmmsearch --tblout GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85ca7018-79a9-46e4-ace4-4f1e4ce840ca/dqc_reference/reference_markers.hmm GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/protein.faa > /dev/null
[2023-06-30 08:19:46,826] [INFO] Task succeeded: HMMsearch
[2023-06-30 08:19:46,828] [INFO] Found 6/6 markers.
[2023-06-30 08:19:46,840] [INFO] Query marker FASTA was written to GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/markers.fasta
[2023-06-30 08:19:46,841] [INFO] Task started: Blastn
[2023-06-30 08:19:46,841] [INFO] Running command: blastn -query GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/markers.fasta -db /var/lib/cwl/stg85ca7018-79a9-46e4-ace4-4f1e4ce840ca/dqc_reference/reference_markers.fasta -out GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:19:48,874] [INFO] Task succeeded: Blastn
[2023-06-30 08:19:48,878] [INFO] Selected 18 target genomes.
[2023-06-30 08:19:48,879] [INFO] Target genome list was writen to GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/target_genomes.txt
[2023-06-30 08:19:48,887] [INFO] Task started: fastANI
[2023-06-30 08:19:48,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg12daa2bd-e005-4e7b-8091-7bf9ed9dbb05/GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna.gz --refList GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/target_genomes.txt --output GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 08:19:57,707] [INFO] Task succeeded: fastANI
[2023-06-30 08:19:57,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85ca7018-79a9-46e4-ace4-4f1e4ce840ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 08:19:57,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85ca7018-79a9-46e4-ace4-4f1e4ce840ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 08:19:57,709] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 08:19:57,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 08:19:57,710] [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 08:19:57,712] [INFO] DFAST Taxonomy check result was written to GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/tc_result.tsv
[2023-06-30 08:19:57,712] [INFO] ===== Taxonomy check completed =====
[2023-06-30 08:19:57,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 08:19:57,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85ca7018-79a9-46e4-ace4-4f1e4ce840ca/dqc_reference/checkm_data
[2023-06-30 08:19:57,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 08:19:57,734] [INFO] Task started: CheckM
[2023-06-30 08:19:57,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/checkm_input GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/checkm_result
[2023-06-30 08:20:12,818] [INFO] Task succeeded: CheckM
[2023-06-30 08:20:12,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 08:20:12,840] [INFO] ===== Completeness check finished =====
[2023-06-30 08:20:12,841] [INFO] ===== Start GTDB Search =====
[2023-06-30 08:20:12,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/markers.fasta)
[2023-06-30 08:20:12,842] [INFO] Task started: Blastn
[2023-06-30 08:20:12,842] [INFO] Running command: blastn -query GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/markers.fasta -db /var/lib/cwl/stg85ca7018-79a9-46e4-ace4-4f1e4ce840ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:20:13,643] [INFO] Task succeeded: Blastn
[2023-06-30 08:20:13,648] [INFO] Selected 13 target genomes.
[2023-06-30 08:20:13,648] [INFO] Target genome list was writen to GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 08:20:13,652] [INFO] Task started: fastANI
[2023-06-30 08:20:13,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg12daa2bd-e005-4e7b-8091-7bf9ed9dbb05/GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna.gz --refList GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/target_genomes_gtdb.txt --output GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:20:15,659] [INFO] Task succeeded: fastANI
[2023-06-30 08:20:15,666] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 08:20:15,667] [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_903823865.1	s__Bog-1340 sp903823865	99.916	202	213	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__GWA1-40-21;g__Bog-1340	95.0	99.90	99.84	0.95	0.84	12	conclusive
GCA_903831595.1	s__Bog-1340 sp903831595	85.1383	161	213	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__GWA1-40-21;g__Bog-1340	95.0	99.98	99.98	0.96	0.96	2	-
GCA_903850545.1	s__Bog-1340 sp903850545	78.6475	97	213	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__GWA1-40-21;g__Bog-1340	95.0	99.96	99.96	0.84	0.84	2	-
GCA_003142075.1	s__Bog-1340 sp003142075	78.6416	80	213	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__GWA1-40-21;g__Bog-1340	95.0	99.90	99.90	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-30 08:20:15,669] [INFO] GTDB search result was written to GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/result_gtdb.tsv
[2023-06-30 08:20:15,670] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:20:15,673] [INFO] DFAST_QC result json was written to GCA_903907565.1_freshwater_MAG_---_AM-lipid-01-D9_bin-0303_genomic.fna/dqc_result.json
[2023-06-30 08:20:15,673] [INFO] DFAST_QC completed!
[2023-06-30 08:20:15,673] [INFO] Total running time: 0h0m34s