[2023-06-18 20:10:45,221] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:10:45,225] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:10:45,226] [INFO] DQC Reference Directory: /var/lib/cwl/stg05b51d68-bfd3-4ec7-a2fd-4707c928152e/dqc_reference
[2023-06-18 20:10:47,053] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:10:47,054] [INFO] Task started: Prodigal
[2023-06-18 20:10:47,054] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8869f5f-945c-4380-b543-63ac13ddbfd6/GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:10:55,078] [INFO] Task succeeded: Prodigal
[2023-06-18 20:10:55,078] [INFO] Task started: HMMsearch
[2023-06-18 20:10:55,078] [INFO] Running command: hmmsearch --tblout GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05b51d68-bfd3-4ec7-a2fd-4707c928152e/dqc_reference/reference_markers.hmm GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:10:55,301] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:10:55,302] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8869f5f-945c-4380-b543-63ac13ddbfd6/GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-18 20:10:55,325] [INFO] Query marker FASTA was written to GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 20:10:55,325] [INFO] Task started: Blastn
[2023-06-18 20:10:55,325] [INFO] Running command: blastn -query GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b51d68-bfd3-4ec7-a2fd-4707c928152e/dqc_reference/reference_markers.fasta -out GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:10:55,899] [INFO] Task succeeded: Blastn
[2023-06-18 20:10:55,904] [INFO] Selected 26 target genomes.
[2023-06-18 20:10:55,904] [INFO] Target genome list was writen to GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 20:10:55,909] [INFO] Task started: fastANI
[2023-06-18 20:10:55,910] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8869f5f-945c-4380-b543-63ac13ddbfd6/GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:11:10,470] [INFO] Task succeeded: fastANI
[2023-06-18 20:11:10,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05b51d68-bfd3-4ec7-a2fd-4707c928152e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:11:10,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05b51d68-bfd3-4ec7-a2fd-4707c928152e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:11:10,473] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:11:10,473] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:11:10,473] [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
--------------------------------------------------------------------------------
[2023-06-18 20:11:10,475] [INFO] DFAST Taxonomy check result was written to GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 20:11:10,476] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:11:10,476] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:11:10,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05b51d68-bfd3-4ec7-a2fd-4707c928152e/dqc_reference/checkm_data
[2023-06-18 20:11:10,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:11:10,504] [INFO] Task started: CheckM
[2023-06-18 20:11:10,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 20:11:39,897] [INFO] Task succeeded: CheckM
[2023-06-18 20:11:39,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 9.26%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-18 20:11:39,920] [INFO] ===== Completeness check finished =====
[2023-06-18 20:11:39,920] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:11:39,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 20:11:39,921] [INFO] Task started: Blastn
[2023-06-18 20:11:39,921] [INFO] Running command: blastn -query GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b51d68-bfd3-4ec7-a2fd-4707c928152e/dqc_reference/reference_markers_gtdb.fasta -out GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:11:40,711] [INFO] Task succeeded: Blastn
[2023-06-18 20:11:40,715] [INFO] Selected 10 target genomes.
[2023-06-18 20:11:40,715] [INFO] Target genome list was writen to GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:11:40,743] [INFO] Task started: fastANI
[2023-06-18 20:11:40,743] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8869f5f-945c-4380-b543-63ac13ddbfd6/GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:11:44,465] [INFO] Task succeeded: fastANI
[2023-06-18 20:11:44,479] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 20:11:44,479] [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_017647785.1	s__Onthomorpha sp017647785	86.7779	457	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559135.1	s__Onthomorpha sp017559135	85.0468	487	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017647065.1	s__Onthomorpha sp017647065	85.0055	313	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002358855.1	s__Onthomorpha sp002358855	84.65	438	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	96.75	96.51	0.86	0.83	6	-
GCA_017632095.1	s__Onthomorpha sp017632095	77.4828	81	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837565.1	s__UBA10566 sp012837565	77.1278	51	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296345.1	s__Onthomorpha sp016296345	76.8155	62	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	97.30	97.30	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-18 20:11:44,481] [INFO] GTDB search result was written to GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 20:11:44,482] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:11:44,484] [INFO] DFAST_QC result json was written to GCA_937906975.1_SRR6425764_bin.46_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 20:11:44,485] [INFO] DFAST_QC completed!
[2023-06-18 20:11:44,485] [INFO] Total running time: 0h0m59s