[2023-06-08 04:30:11,215] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:30:11,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:30:11,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg45d807d9-a287-4863-a831-805ebc596859/dqc_reference
[2023-06-08 04:30:12,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:30:12,539] [INFO] Task started: Prodigal
[2023-06-08 04:30:12,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg25194b71-cc0f-41e2-b4b1-25f03b150a7b/GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:30:14,561] [INFO] Task succeeded: Prodigal
[2023-06-08 04:30:14,562] [INFO] Task started: HMMsearch
[2023-06-08 04:30:14,562] [INFO] Running command: hmmsearch --tblout GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45d807d9-a287-4863-a831-805ebc596859/dqc_reference/reference_markers.hmm GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:30:14,742] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:30:14,743] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg25194b71-cc0f-41e2-b4b1-25f03b150a7b/GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 04:30:14,760] [INFO] Query marker FASTA was written to GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 04:30:14,760] [INFO] Task started: Blastn
[2023-06-08 04:30:14,761] [INFO] Running command: blastn -query GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d807d9-a287-4863-a831-805ebc596859/dqc_reference/reference_markers.fasta -out GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:30:15,324] [INFO] Task succeeded: Blastn
[2023-06-08 04:30:15,331] [INFO] Selected 17 target genomes.
[2023-06-08 04:30:15,332] [INFO] Target genome list was writen to GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 04:30:15,334] [INFO] Task started: fastANI
[2023-06-08 04:30:15,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg25194b71-cc0f-41e2-b4b1-25f03b150a7b/GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:30:28,061] [INFO] Task succeeded: fastANI
[2023-06-08 04:30:28,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45d807d9-a287-4863-a831-805ebc596859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:30:28,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45d807d9-a287-4863-a831-805ebc596859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:30:28,064] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:30:28,064] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 04:30:28,064] [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
--------------------------------------------------------------------------------
[2023-06-08 04:30:28,066] [INFO] DFAST Taxonomy check result was written to GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 04:30:28,067] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:30:28,067] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:30:28,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45d807d9-a287-4863-a831-805ebc596859/dqc_reference/checkm_data
[2023-06-08 04:30:28,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:30:28,097] [INFO] Task started: CheckM
[2023-06-08 04:30:28,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 04:30:43,292] [INFO] Task succeeded: CheckM
[2023-06-08 04:30:43,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:30:43,323] [INFO] ===== Completeness check finished =====
[2023-06-08 04:30:43,323] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:30:43,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 04:30:43,323] [INFO] Task started: Blastn
[2023-06-08 04:30:43,323] [INFO] Running command: blastn -query GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d807d9-a287-4863-a831-805ebc596859/dqc_reference/reference_markers_gtdb.fasta -out GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:30:44,023] [INFO] Task succeeded: Blastn
[2023-06-08 04:30:44,027] [INFO] Selected 18 target genomes.
[2023-06-08 04:30:44,027] [INFO] Target genome list was writen to GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:30:44,031] [INFO] Task started: fastANI
[2023-06-08 04:30:44,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg25194b71-cc0f-41e2-b4b1-25f03b150a7b/GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:30:51,353] [INFO] Task succeeded: fastANI
[2023-06-08 04:30:51,361] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 04:30:51,362] [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
GCF_002100115.1	s__Anaerovibrio sp002100115	78.6641	52	239	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548165.1	s__Anaerovibrio sp900548165	77.7844	58	239	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	96.97	96.65	0.86	0.85	4	-
GCA_017390245.1	s__Anaerovibrio sp017390245	77.382	51	239	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:30:51,364] [INFO] GTDB search result was written to GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 04:30:51,364] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:30:51,368] [INFO] DFAST_QC result json was written to GCA_945948665.1_SRR15057930_bin.15_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 04:30:51,368] [INFO] DFAST_QC completed!
[2023-06-08 04:30:51,368] [INFO] Total running time: 0h0m40s