[2023-07-01 02:12:38,763] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:12:38,767] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:12:38,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgee41caed-26a7-410d-be87-59995365ca73/dqc_reference
[2023-07-01 02:12:40,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:12:40,633] [INFO] Task started: Prodigal
[2023-07-01 02:12:40,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8932f29-6f1e-4a0d-ba8f-2b4cf541fe30/GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna.gz | prodigal -d GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/cds.fna -a GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:12:44,505] [INFO] Task succeeded: Prodigal
[2023-07-01 02:12:44,506] [INFO] Task started: HMMsearch
[2023-07-01 02:12:44,506] [INFO] Running command: hmmsearch --tblout GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee41caed-26a7-410d-be87-59995365ca73/dqc_reference/reference_markers.hmm GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:12:44,694] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:12:44,696] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgf8932f29-6f1e-4a0d-ba8f-2b4cf541fe30/GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna.gz]
[2023-07-01 02:12:44,718] [INFO] Query marker FASTA was written to GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/markers.fasta
[2023-07-01 02:12:44,718] [INFO] Task started: Blastn
[2023-07-01 02:12:44,718] [INFO] Running command: blastn -query GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/markers.fasta -db /var/lib/cwl/stgee41caed-26a7-410d-be87-59995365ca73/dqc_reference/reference_markers.fasta -out GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:12:45,285] [INFO] Task succeeded: Blastn
[2023-07-01 02:12:45,289] [INFO] Selected 5 target genomes.
[2023-07-01 02:12:45,289] [INFO] Target genome list was writen to GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/target_genomes.txt
[2023-07-01 02:12:45,290] [INFO] Task started: fastANI
[2023-07-01 02:12:45,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8932f29-6f1e-4a0d-ba8f-2b4cf541fe30/GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna.gz --refList GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/target_genomes.txt --output GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:12:48,943] [INFO] Task succeeded: fastANI
[2023-07-01 02:12:48,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee41caed-26a7-410d-be87-59995365ca73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:12:48,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee41caed-26a7-410d-be87-59995365ca73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:12:48,947] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:12:48,947] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:12:48,947] [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
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	77.6895	50	135	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:12:48,964] [INFO] DFAST Taxonomy check result was written to GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/tc_result.tsv
[2023-07-01 02:12:48,964] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:12:48,965] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:12:48,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee41caed-26a7-410d-be87-59995365ca73/dqc_reference/checkm_data
[2023-07-01 02:12:48,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:12:48,987] [INFO] Task started: CheckM
[2023-07-01 02:12:48,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/checkm_input GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/checkm_result
[2023-07-01 02:13:08,708] [INFO] Task succeeded: CheckM
[2023-07-01 02:13:08,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 27.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:13:08,729] [INFO] ===== Completeness check finished =====
[2023-07-01 02:13:08,729] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:13:08,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/markers.fasta)
[2023-07-01 02:13:08,730] [INFO] Task started: Blastn
[2023-07-01 02:13:08,730] [INFO] Running command: blastn -query GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/markers.fasta -db /var/lib/cwl/stgee41caed-26a7-410d-be87-59995365ca73/dqc_reference/reference_markers_gtdb.fasta -out GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:13:09,253] [INFO] Task succeeded: Blastn
[2023-07-01 02:13:09,257] [INFO] Selected 5 target genomes.
[2023-07-01 02:13:09,258] [INFO] Target genome list was writen to GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:13:09,260] [INFO] Task started: fastANI
[2023-07-01 02:13:09,261] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8932f29-6f1e-4a0d-ba8f-2b4cf541fe30/GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna.gz --refList GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/target_genomes_gtdb.txt --output GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:13:12,574] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:12,578] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 02:13:12,578] [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_903941205.1	s__Polaromonas sp903941205	78.6863	59	135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:13:12,581] [INFO] GTDB search result was written to GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/result_gtdb.tsv
[2023-07-01 02:13:12,581] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:13:12,584] [INFO] DFAST_QC result json was written to GCA_903883735.1_freshwater_MAG_---_LinL2_bin-0632_genomic.fna/dqc_result.json
[2023-07-01 02:13:12,584] [INFO] DFAST_QC completed!
[2023-07-01 02:13:12,584] [INFO] Total running time: 0h0m34s