[2023-06-30 06:33:15,331] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:33:15,334] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:33:15,334] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3194661-8fd4-47e4-91f5-a5dab7d974cc/dqc_reference
[2023-06-30 06:33:16,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:33:16,814] [INFO] Task started: Prodigal
[2023-06-30 06:33:16,814] [INFO] Running command: gunzip -c /var/lib/cwl/stgc07681d0-a533-4703-9d94-5bf8673d60be/GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna.gz | prodigal -d GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/cds.fna -a GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:33:22,707] [INFO] Task succeeded: Prodigal
[2023-06-30 06:33:22,707] [INFO] Task started: HMMsearch
[2023-06-30 06:33:22,707] [INFO] Running command: hmmsearch --tblout GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3194661-8fd4-47e4-91f5-a5dab7d974cc/dqc_reference/reference_markers.hmm GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:33:22,959] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:33:22,960] [INFO] Found 6/6 markers.
[2023-06-30 06:33:22,995] [INFO] Query marker FASTA was written to GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/markers.fasta
[2023-06-30 06:33:22,996] [INFO] Task started: Blastn
[2023-06-30 06:33:22,996] [INFO] Running command: blastn -query GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3194661-8fd4-47e4-91f5-a5dab7d974cc/dqc_reference/reference_markers.fasta -out GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:33:23,636] [INFO] Task succeeded: Blastn
[2023-06-30 06:33:23,650] [INFO] Selected 33 target genomes.
[2023-06-30 06:33:23,651] [INFO] Target genome list was writen to GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/target_genomes.txt
[2023-06-30 06:33:23,660] [INFO] Task started: fastANI
[2023-06-30 06:33:23,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07681d0-a533-4703-9d94-5bf8673d60be/GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna.gz --refList GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/target_genomes.txt --output GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:33:44,256] [INFO] Task succeeded: fastANI
[2023-06-30 06:33:44,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3194661-8fd4-47e4-91f5-a5dab7d974cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:33:44,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3194661-8fd4-47e4-91f5-a5dab7d974cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:33:44,258] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:33:44,258] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 06:33:44,259] [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 06:33:44,261] [INFO] DFAST Taxonomy check result was written to GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/tc_result.tsv
[2023-06-30 06:33:44,262] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:33:44,262] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:33:44,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3194661-8fd4-47e4-91f5-a5dab7d974cc/dqc_reference/checkm_data
[2023-06-30 06:33:44,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:33:44,294] [INFO] Task started: CheckM
[2023-06-30 06:33:44,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/checkm_input GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/checkm_result
[2023-06-30 06:34:07,385] [INFO] Task succeeded: CheckM
[2023-06-30 06:34:07,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.82%
Contamintation: 9.09%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 06:34:07,410] [INFO] ===== Completeness check finished =====
[2023-06-30 06:34:07,410] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:34:07,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/markers.fasta)
[2023-06-30 06:34:07,411] [INFO] Task started: Blastn
[2023-06-30 06:34:07,411] [INFO] Running command: blastn -query GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3194661-8fd4-47e4-91f5-a5dab7d974cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:34:08,286] [INFO] Task succeeded: Blastn
[2023-06-30 06:34:08,290] [INFO] Selected 8 target genomes.
[2023-06-30 06:34:08,291] [INFO] Target genome list was writen to GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:34:08,294] [INFO] Task started: fastANI
[2023-06-30 06:34:08,294] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07681d0-a533-4703-9d94-5bf8673d60be/GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna.gz --refList GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/target_genomes_gtdb.txt --output GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:34:11,178] [INFO] Task succeeded: fastANI
[2023-06-30 06:34:11,187] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 06:34:11,187] [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_009693615.1	s__Sediminibacterium sp009693615	90.8914	239	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205585.1	s__Sediminibacterium sp013205585	89.8628	252	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825095.1	s__Sediminibacterium sp903825095	89.6522	216	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.41	98.41	0.71	0.71	2	-
GCA_007280515.1	s__Sediminibacterium sp007280515	88.904	269	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009928005.1	s__Sediminibacterium sp009928005	87.3392	279	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.65	99.49	0.90	0.88	3	-
GCA_903854725.1	s__Sediminibacterium sp903854725	83.2795	272	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.67	99.52	0.89	0.86	5	-
GCA_903865435.1	s__Sediminibacterium sp903865435	82.8538	231	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.68	99.46	0.94	0.90	16	-
GCA_903847655.1	s__Sediminibacterium sp903847655	81.9503	187	328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:34:11,189] [INFO] GTDB search result was written to GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/result_gtdb.tsv
[2023-06-30 06:34:11,189] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:34:11,192] [INFO] DFAST_QC result json was written to GCA_903856565.1_freshwater_MAG_---_Erken-D2_bin-0351_genomic.fna/dqc_result.json
[2023-06-30 06:34:11,192] [INFO] DFAST_QC completed!
[2023-06-30 06:34:11,192] [INFO] Total running time: 0h0m56s