[2023-06-08 05:14:18,620] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:14:18,621] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:14:18,621] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a7a7db9-7445-4058-9783-fc7ccf6c71f0/dqc_reference
[2023-06-08 05:14:20,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:14:20,248] [INFO] Task started: Prodigal
[2023-06-08 05:14:20,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg159d75ee-87d9-4db7-85fe-e6e63f44256a/GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:14:28,341] [INFO] Task succeeded: Prodigal
[2023-06-08 05:14:28,341] [INFO] Task started: HMMsearch
[2023-06-08 05:14:28,341] [INFO] Running command: hmmsearch --tblout GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a7a7db9-7445-4058-9783-fc7ccf6c71f0/dqc_reference/reference_markers.hmm GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:14:28,535] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:14:28,537] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg159d75ee-87d9-4db7-85fe-e6e63f44256a/GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 05:14:28,555] [INFO] Query marker FASTA was written to GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 05:14:28,556] [INFO] Task started: Blastn
[2023-06-08 05:14:28,556] [INFO] Running command: blastn -query GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a7a7db9-7445-4058-9783-fc7ccf6c71f0/dqc_reference/reference_markers.fasta -out GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:14:29,127] [INFO] Task succeeded: Blastn
[2023-06-08 05:14:29,132] [INFO] Selected 20 target genomes.
[2023-06-08 05:14:29,133] [INFO] Target genome list was writen to GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 05:14:29,137] [INFO] Task started: fastANI
[2023-06-08 05:14:29,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg159d75ee-87d9-4db7-85fe-e6e63f44256a/GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:14:38,772] [INFO] Task succeeded: fastANI
[2023-06-08 05:14:38,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a7a7db9-7445-4058-9783-fc7ccf6c71f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:14:38,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a7a7db9-7445-4058-9783-fc7ccf6c71f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:14:38,775] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:14:38,775] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 05:14:38,776] [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 05:14:38,778] [INFO] DFAST Taxonomy check result was written to GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 05:14:38,778] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:14:38,778] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:14:38,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a7a7db9-7445-4058-9783-fc7ccf6c71f0/dqc_reference/checkm_data
[2023-06-08 05:14:38,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:14:38,803] [INFO] Task started: CheckM
[2023-06-08 05:14:38,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 05:15:07,425] [INFO] Task succeeded: CheckM
[2023-06-08 05:15:07,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:15:07,442] [INFO] ===== Completeness check finished =====
[2023-06-08 05:15:07,442] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:15:07,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 05:15:07,443] [INFO] Task started: Blastn
[2023-06-08 05:15:07,443] [INFO] Running command: blastn -query GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a7a7db9-7445-4058-9783-fc7ccf6c71f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:15:08,186] [INFO] Task succeeded: Blastn
[2023-06-08 05:15:08,190] [INFO] Selected 9 target genomes.
[2023-06-08 05:15:08,191] [INFO] Target genome list was writen to GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:15:08,194] [INFO] Task started: fastANI
[2023-06-08 05:15:08,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg159d75ee-87d9-4db7-85fe-e6e63f44256a/GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:15:12,623] [INFO] Task succeeded: fastANI
[2023-06-08 05:15:12,637] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:15:12,637] [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_902776565.1	s__Bact-19 sp902776565	96.0794	320	363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	96.47	95.98	0.86	0.82	3	conclusive
GCA_902762455.1	s__Bact-19 sp902762455	93.8702	279	363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	95.34	95.27	0.87	0.87	3	-
GCA_017620015.1	s__Bact-19 sp017620015	91.0596	323	363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800045.1	s__Bact-19 sp902800045	87.8138	267	363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790405.1	s__Bact-19 sp902790405	86.9922	250	363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617125.1	s__Bact-19 sp017617125	84.906	257	363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234755.1	s__Bact-19 sp905234755	83.8327	265	363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:15:12,639] [INFO] GTDB search result was written to GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 05:15:12,639] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:15:12,642] [INFO] DFAST_QC result json was written to GCA_947166495.1_SRR8387716_bin.53_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 05:15:12,642] [INFO] DFAST_QC completed!
[2023-06-08 05:15:12,642] [INFO] Total running time: 0h0m54s