[2023-06-30 16:54:22,712] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:54:22,715] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:54:22,715] [INFO] DQC Reference Directory: /var/lib/cwl/stge042fe96-06d1-414a-9d16-158587fa5a7b/dqc_reference
[2023-06-30 16:54:25,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:54:25,032] [INFO] Task started: Prodigal
[2023-06-30 16:54:25,032] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4cf0248-2cf2-4c9a-b188-bc9fa6c865f0/GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna.gz | prodigal -d GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/cds.fna -a GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:54:38,050] [INFO] Task succeeded: Prodigal
[2023-06-30 16:54:38,050] [INFO] Task started: HMMsearch
[2023-06-30 16:54:38,050] [INFO] Running command: hmmsearch --tblout GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge042fe96-06d1-414a-9d16-158587fa5a7b/dqc_reference/reference_markers.hmm GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:54:38,258] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:54:38,260] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb4cf0248-2cf2-4c9a-b188-bc9fa6c865f0/GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna.gz]
[2023-06-30 16:54:38,289] [INFO] Query marker FASTA was written to GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/markers.fasta
[2023-06-30 16:54:38,290] [INFO] Task started: Blastn
[2023-06-30 16:54:38,290] [INFO] Running command: blastn -query GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/markers.fasta -db /var/lib/cwl/stge042fe96-06d1-414a-9d16-158587fa5a7b/dqc_reference/reference_markers.fasta -out GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:54:38,823] [INFO] Task succeeded: Blastn
[2023-06-30 16:54:38,828] [INFO] Selected 10 target genomes.
[2023-06-30 16:54:38,828] [INFO] Target genome list was writen to GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/target_genomes.txt
[2023-06-30 16:54:38,832] [INFO] Task started: fastANI
[2023-06-30 16:54:38,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4cf0248-2cf2-4c9a-b188-bc9fa6c865f0/GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna.gz --refList GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/target_genomes.txt --output GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:54:44,689] [INFO] Task succeeded: fastANI
[2023-06-30 16:54:44,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge042fe96-06d1-414a-9d16-158587fa5a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:54:44,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge042fe96-06d1-414a-9d16-158587fa5a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:54:44,692] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:54:44,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 16:54:44,693] [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 16:54:44,696] [INFO] DFAST Taxonomy check result was written to GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/tc_result.tsv
[2023-06-30 16:54:44,697] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:54:44,698] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:54:44,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge042fe96-06d1-414a-9d16-158587fa5a7b/dqc_reference/checkm_data
[2023-06-30 16:54:44,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:54:44,741] [INFO] Task started: CheckM
[2023-06-30 16:54:44,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/checkm_input GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/checkm_result
[2023-06-30 16:55:27,527] [INFO] Task succeeded: CheckM
[2023-06-30 16:55:27,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:55:27,548] [INFO] ===== Completeness check finished =====
[2023-06-30 16:55:27,548] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:55:27,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/markers.fasta)
[2023-06-30 16:55:27,549] [INFO] Task started: Blastn
[2023-06-30 16:55:27,549] [INFO] Running command: blastn -query GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/markers.fasta -db /var/lib/cwl/stge042fe96-06d1-414a-9d16-158587fa5a7b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:55:28,227] [INFO] Task succeeded: Blastn
[2023-06-30 16:55:28,231] [INFO] Selected 6 target genomes.
[2023-06-30 16:55:28,231] [INFO] Target genome list was writen to GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:55:28,234] [INFO] Task started: fastANI
[2023-06-30 16:55:28,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4cf0248-2cf2-4c9a-b188-bc9fa6c865f0/GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna.gz --refList GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/target_genomes_gtdb.txt --output GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:55:32,740] [INFO] Task succeeded: fastANI
[2023-06-30 16:55:32,750] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:55:32,751] [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_903926565.1	s__CAIVAT01 sp903926565	99.6588	568	606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.94	99.94	0.97	0.97	2	conclusive
GCA_903828645.1	s__CAIVAT01 sp903828645	78.145	190	606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.44	99.32	0.88	0.87	3	-
GCA_903959905.1	s__CAIVAT01 sp903959905	78.0453	170	606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.98	99.96	0.97	0.97	6	-
GCA_903875045.1	s__CAIVAT01 sp903875045	77.8952	198	606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:55:32,753] [INFO] GTDB search result was written to GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/result_gtdb.tsv
[2023-06-30 16:55:32,753] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:55:32,756] [INFO] DFAST_QC result json was written to GCA_903907365.1_freshwater_MAG_---_Ja1-D5_bin-345_genomic.fna/dqc_result.json
[2023-06-30 16:55:32,756] [INFO] DFAST_QC completed!
[2023-06-30 16:55:32,756] [INFO] Total running time: 0h1m10s