[2023-06-07 18:22:32,995] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:22:32,997] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:22:32,997] [INFO] DQC Reference Directory: /var/lib/cwl/stgb348072d-a5fa-4e5e-9e36-fe01b65fecf5/dqc_reference
[2023-06-07 18:22:34,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:22:34,210] [INFO] Task started: Prodigal
[2023-06-07 18:22:34,210] [INFO] Running command: gunzip -c /var/lib/cwl/stga653968a-9d46-4b34-a1e7-3a267f7ed873/GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:22:37,758] [INFO] Task succeeded: Prodigal
[2023-06-07 18:22:37,758] [INFO] Task started: HMMsearch
[2023-06-07 18:22:37,758] [INFO] Running command: hmmsearch --tblout GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb348072d-a5fa-4e5e-9e36-fe01b65fecf5/dqc_reference/reference_markers.hmm GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:22:37,984] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:22:37,986] [INFO] Found 6/6 markers.
[2023-06-07 18:22:38,006] [INFO] Query marker FASTA was written to GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 18:22:38,007] [INFO] Task started: Blastn
[2023-06-07 18:22:38,007] [INFO] Running command: blastn -query GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb348072d-a5fa-4e5e-9e36-fe01b65fecf5/dqc_reference/reference_markers.fasta -out GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:22:38,648] [INFO] Task succeeded: Blastn
[2023-06-07 18:22:38,659] [INFO] Selected 28 target genomes.
[2023-06-07 18:22:38,659] [INFO] Target genome list was writen to GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 18:22:38,660] [INFO] Task started: fastANI
[2023-06-07 18:22:38,661] [INFO] Running command: fastANI --query /var/lib/cwl/stga653968a-9d46-4b34-a1e7-3a267f7ed873/GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:22:53,440] [INFO] Task succeeded: fastANI
[2023-06-07 18:22:53,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb348072d-a5fa-4e5e-9e36-fe01b65fecf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:22:53,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb348072d-a5fa-4e5e-9e36-fe01b65fecf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:22:53,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:22:53,443] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 18:22:53,443] [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
--------------------------------------------------------------------------------
[2023-06-07 18:22:53,445] [INFO] DFAST Taxonomy check result was written to GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 18:22:53,446] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:22:53,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:22:53,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb348072d-a5fa-4e5e-9e36-fe01b65fecf5/dqc_reference/checkm_data
[2023-06-07 18:22:53,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:22:53,471] [INFO] Task started: CheckM
[2023-06-07 18:22:53,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 18:23:11,510] [INFO] Task succeeded: CheckM
[2023-06-07 18:23:11,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:23:11,531] [INFO] ===== Completeness check finished =====
[2023-06-07 18:23:11,531] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:23:11,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 18:23:11,532] [INFO] Task started: Blastn
[2023-06-07 18:23:11,532] [INFO] Running command: blastn -query GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb348072d-a5fa-4e5e-9e36-fe01b65fecf5/dqc_reference/reference_markers_gtdb.fasta -out GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:23:12,608] [INFO] Task succeeded: Blastn
[2023-06-07 18:23:12,613] [INFO] Selected 24 target genomes.
[2023-06-07 18:23:12,613] [INFO] Target genome list was writen to GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:23:12,615] [INFO] Task started: fastANI
[2023-06-07 18:23:12,615] [INFO] Running command: fastANI --query /var/lib/cwl/stga653968a-9d46-4b34-a1e7-3a267f7ed873/GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:23:19,425] [INFO] Task succeeded: fastANI
[2023-06-07 18:23:19,438] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 18:23:19,438] [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_900767645.1	s__CAAFZY01 sp900767645	77.3219	66	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAAFZY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626035.1	s__JAGAJR01 sp017626035	77.3035	67	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAGAJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585375.1	s__MGBC133411 sp910585375	77.0079	53	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762565.1	s__51-20 sp900762565	76.9114	61	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062345.1	s__JAFTYO01 sp015062345	76.7099	70	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAFTYO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917125.1	s__Scatocola faecipullorum	76.7092	53	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	98.98	98.59	0.91	0.85	10	-
GCA_900538765.1	s__HGM16780 sp900538765	76.6628	50	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	98.94	98.77	0.94	0.91	4	-
GCA_017528205.1	s__RUG410 sp017528205	76.5813	64	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__RUG410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577205.1	s__Scatocola sp910577205	76.5711	52	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769705.1	s__RUG410 sp900769705	76.5379	60	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__RUG410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017464685.1	s__JAFTYO01 sp017464685	76.2927	51	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAFTYO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 18:23:19,440] [INFO] GTDB search result was written to GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 18:23:19,441] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:23:19,443] [INFO] DFAST_QC result json was written to GCA_945949705.1_SRR11489746_bin.35_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 18:23:19,444] [INFO] DFAST_QC completed!
[2023-06-07 18:23:19,444] [INFO] Total running time: 0h0m46s