[2023-06-08 19:51:30,267] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:51:30,269] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:51:30,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgf357d74c-5c1e-4dc2-ab52-5503638b6989/dqc_reference
[2023-06-08 19:51:31,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:51:31,525] [INFO] Task started: Prodigal
[2023-06-08 19:51:31,525] [INFO] Running command: gunzip -c /var/lib/cwl/stgf966c175-9011-4009-a484-a303a26a65bf/GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:51:37,671] [INFO] Task succeeded: Prodigal
[2023-06-08 19:51:37,672] [INFO] Task started: HMMsearch
[2023-06-08 19:51:37,672] [INFO] Running command: hmmsearch --tblout GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf357d74c-5c1e-4dc2-ab52-5503638b6989/dqc_reference/reference_markers.hmm GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:51:37,968] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:51:37,969] [INFO] Found 6/6 markers.
[2023-06-08 19:51:37,993] [INFO] Query marker FASTA was written to GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:51:37,994] [INFO] Task started: Blastn
[2023-06-08 19:51:37,994] [INFO] Running command: blastn -query GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf357d74c-5c1e-4dc2-ab52-5503638b6989/dqc_reference/reference_markers.fasta -out GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:51:38,695] [INFO] Task succeeded: Blastn
[2023-06-08 19:51:38,699] [INFO] Selected 17 target genomes.
[2023-06-08 19:51:38,700] [INFO] Target genome list was writen to GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:51:38,704] [INFO] Task started: fastANI
[2023-06-08 19:51:38,704] [INFO] Running command: fastANI --query /var/lib/cwl/stgf966c175-9011-4009-a484-a303a26a65bf/GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:51:48,305] [INFO] Task succeeded: fastANI
[2023-06-08 19:51:48,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf357d74c-5c1e-4dc2-ab52-5503638b6989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:51:48,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf357d74c-5c1e-4dc2-ab52-5503638b6989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:51:48,310] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:51:48,310] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 19:51:48,310] [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 19:51:48,312] [INFO] DFAST Taxonomy check result was written to GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:51:48,313] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:51:48,313] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:51:48,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf357d74c-5c1e-4dc2-ab52-5503638b6989/dqc_reference/checkm_data
[2023-06-08 19:51:48,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:51:48,347] [INFO] Task started: CheckM
[2023-06-08 19:51:48,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:52:14,078] [INFO] Task succeeded: CheckM
[2023-06-08 19:52:14,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:52:14,102] [INFO] ===== Completeness check finished =====
[2023-06-08 19:52:14,102] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:52:14,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:52:14,103] [INFO] Task started: Blastn
[2023-06-08 19:52:14,103] [INFO] Running command: blastn -query GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf357d74c-5c1e-4dc2-ab52-5503638b6989/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:52:15,189] [INFO] Task succeeded: Blastn
[2023-06-08 19:52:15,193] [INFO] Selected 14 target genomes.
[2023-06-08 19:52:15,193] [INFO] Target genome list was writen to GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:52:15,199] [INFO] Task started: fastANI
[2023-06-08 19:52:15,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgf966c175-9011-4009-a484-a303a26a65bf/GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:52:21,428] [INFO] Task succeeded: fastANI
[2023-06-08 19:52:21,442] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:52:21,443] [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_900319455.1	s__CAG-177 sp900319455	98.0438	530	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	98.34	97.29	0.87	0.72	5	conclusive
GCA_017428625.1	s__CAG-177 sp017428625	83.7451	552	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787025.1	s__CAG-177 sp902787025	82.3423	441	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288315.1	s__CAG-177 sp016288315	81.7636	436	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285645.1	s__CAG-177 sp016285645	79.2266	343	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	97.57	97.01	0.93	0.90	3	-
GCA_017397105.1	s__CAG-177 sp017397105	77.3666	68	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235625.1	s__CAG-177 sp905235625	77.3182	109	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	98.41	98.41	0.91	0.91	2	-
GCA_002315935.1	s__CAG-177 sp002315935	76.8961	60	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435385.1	s__CAG-177 sp017435385	76.8613	65	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409845.1	s__CAG-177 sp017409845	76.4509	64	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	97.27	97.27	0.85	0.85	2	-
GCA_015065965.1	s__CAG-177 sp015065965	76.4326	58	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548045.1	s__CAG-177 sp017548045	76.0667	67	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:52:21,445] [INFO] GTDB search result was written to GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:52:21,445] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:52:21,448] [INFO] DFAST_QC result json was written to GCA_947166045.1_SRR8387714_bin.36_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:52:21,448] [INFO] DFAST_QC completed!
[2023-06-08 19:52:21,448] [INFO] Total running time: 0h0m51s