[2023-06-08 04:30:11,099] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:30:11,108] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:30:11,108] [INFO] DQC Reference Directory: /var/lib/cwl/stgd903c955-866e-401b-b212-baa9cc29fa86/dqc_reference
[2023-06-08 04:30:12,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:30:12,592] [INFO] Task started: Prodigal
[2023-06-08 04:30:12,592] [INFO] Running command: gunzip -c /var/lib/cwl/stge8d6e230-de25-4828-b593-22534536acc0/GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:30:22,424] [INFO] Task succeeded: Prodigal
[2023-06-08 04:30:22,424] [INFO] Task started: HMMsearch
[2023-06-08 04:30:22,424] [INFO] Running command: hmmsearch --tblout GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd903c955-866e-401b-b212-baa9cc29fa86/dqc_reference/reference_markers.hmm GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:30:22,642] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:30:22,643] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge8d6e230-de25-4828-b593-22534536acc0/GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 04:30:22,665] [INFO] Query marker FASTA was written to GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 04:30:22,665] [INFO] Task started: Blastn
[2023-06-08 04:30:22,666] [INFO] Running command: blastn -query GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd903c955-866e-401b-b212-baa9cc29fa86/dqc_reference/reference_markers.fasta -out GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:30:23,225] [INFO] Task succeeded: Blastn
[2023-06-08 04:30:23,231] [INFO] Selected 10 target genomes.
[2023-06-08 04:30:23,232] [INFO] Target genome list was writen to GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 04:30:23,233] [INFO] Task started: fastANI
[2023-06-08 04:30:23,233] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d6e230-de25-4828-b593-22534536acc0/GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:30:28,588] [INFO] Task succeeded: fastANI
[2023-06-08 04:30:28,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd903c955-866e-401b-b212-baa9cc29fa86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:30:28,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd903c955-866e-401b-b212-baa9cc29fa86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:30:28,595] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:30:28,595] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 04:30:28,596] [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
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	78.0941	91	413	95	below_threshold
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	78.0793	92	413	95	below_threshold
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	78.0415	93	413	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.0659	67	413	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.0659	67	413	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:30:28,598] [INFO] DFAST Taxonomy check result was written to GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 04:30:28,598] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:30:28,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:30:28,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd903c955-866e-401b-b212-baa9cc29fa86/dqc_reference/checkm_data
[2023-06-08 04:30:28,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:30:28,638] [INFO] Task started: CheckM
[2023-06-08 04:30:28,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 04:31:01,871] [INFO] Task succeeded: CheckM
[2023-06-08 04:31:01,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:31:01,893] [INFO] ===== Completeness check finished =====
[2023-06-08 04:31:01,893] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:31:01,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 04:31:01,894] [INFO] Task started: Blastn
[2023-06-08 04:31:01,894] [INFO] Running command: blastn -query GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd903c955-866e-401b-b212-baa9cc29fa86/dqc_reference/reference_markers_gtdb.fasta -out GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:31:02,544] [INFO] Task succeeded: Blastn
[2023-06-08 04:31:02,548] [INFO] Selected 11 target genomes.
[2023-06-08 04:31:02,548] [INFO] Target genome list was writen to GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:31:02,551] [INFO] Task started: fastANI
[2023-06-08 04:31:02,551] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d6e230-de25-4828-b593-22534536acc0/GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:31:08,587] [INFO] Task succeeded: fastANI
[2023-06-08 04:31:08,598] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 04:31:08,598] [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_900770835.1	s__Parabacteroides sp900770835	86.8145	305	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793765.1	s__Parabacteroides distasonis_A	78.3645	88	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCF_011038785.1	s__Parabacteroides sp011038785	78.0953	79	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012845.1	s__Parabacteroides distasonis	78.0415	93	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.5445	77	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562445.1	s__Parabacteroides sp004562445	77.269	63	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363715.1	s__Parabacteroides acidifaciens	77.0659	67	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
--------------------------------------------------------------------------------
[2023-06-08 04:31:08,608] [INFO] GTDB search result was written to GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 04:31:08,609] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:31:08,613] [INFO] DFAST_QC result json was written to GCA_945607685.1_SRR14474046_bin.40_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 04:31:08,613] [INFO] DFAST_QC completed!
[2023-06-08 04:31:08,613] [INFO] Total running time: 0h0m58s