[2023-06-30 10:36:35,896] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:36:35,899] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:36:35,899] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd70f5b8-34bf-4756-9f47-ae21c16c3707/dqc_reference
[2023-06-30 10:36:37,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:36:37,176] [INFO] Task started: Prodigal
[2023-06-30 10:36:37,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg081db5cc-1b0f-4792-870a-f2289c285c3b/GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:36:52,340] [INFO] Task succeeded: Prodigal
[2023-06-30 10:36:52,340] [INFO] Task started: HMMsearch
[2023-06-30 10:36:52,341] [INFO] Running command: hmmsearch --tblout GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd70f5b8-34bf-4756-9f47-ae21c16c3707/dqc_reference/reference_markers.hmm GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:36:52,624] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:36:52,626] [INFO] Found 6/6 markers.
[2023-06-30 10:36:52,651] [INFO] Query marker FASTA was written to GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 10:36:52,652] [INFO] Task started: Blastn
[2023-06-30 10:36:52,652] [INFO] Running command: blastn -query GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd70f5b8-34bf-4756-9f47-ae21c16c3707/dqc_reference/reference_markers.fasta -out GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:36:53,246] [INFO] Task succeeded: Blastn
[2023-06-30 10:36:53,250] [INFO] Selected 28 target genomes.
[2023-06-30 10:36:53,251] [INFO] Target genome list was writen to GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 10:36:53,252] [INFO] Task started: fastANI
[2023-06-30 10:36:53,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg081db5cc-1b0f-4792-870a-f2289c285c3b/GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:37:15,226] [INFO] Task succeeded: fastANI
[2023-06-30 10:37:15,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd70f5b8-34bf-4756-9f47-ae21c16c3707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:37:15,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd70f5b8-34bf-4756-9f47-ae21c16c3707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:37:15,228] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:37:15,228] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:37:15,228] [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
--------------------------------------------------------------------------------
[2023-06-30 10:37:15,230] [INFO] DFAST Taxonomy check result was written to GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 10:37:15,231] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:37:15,231] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:37:15,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd70f5b8-34bf-4756-9f47-ae21c16c3707/dqc_reference/checkm_data
[2023-06-30 10:37:15,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:37:15,264] [INFO] Task started: CheckM
[2023-06-30 10:37:15,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 10:38:01,074] [INFO] Task succeeded: CheckM
[2023-06-30 10:38:01,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:38:01,098] [INFO] ===== Completeness check finished =====
[2023-06-30 10:38:01,099] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:38:01,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 10:38:01,099] [INFO] Task started: Blastn
[2023-06-30 10:38:01,099] [INFO] Running command: blastn -query GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd70f5b8-34bf-4756-9f47-ae21c16c3707/dqc_reference/reference_markers_gtdb.fasta -out GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:38:01,901] [INFO] Task succeeded: Blastn
[2023-06-30 10:38:01,907] [INFO] Selected 14 target genomes.
[2023-06-30 10:38:01,907] [INFO] Target genome list was writen to GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:38:01,946] [INFO] Task started: fastANI
[2023-06-30 10:38:01,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg081db5cc-1b0f-4792-870a-f2289c285c3b/GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:38:08,195] [INFO] Task succeeded: fastANI
[2023-06-30 10:38:08,213] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:38:08,213] [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_002392325.1	s__F23-D06 sp002392325	97.124	434	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	97.75	96.78	0.90	0.87	4	conclusive
GCA_017443175.1	s__F23-D06 sp017443175	81.3933	244	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	96.79	96.69	0.73	0.72	3	-
GCA_017554325.1	s__F23-D06 sp017554325	81.2301	406	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233745.1	s__F23-D06 sp905233745	81.157	364	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285145.1	s__F23-D06 sp016285145	79.4673	251	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540505.1	s__F23-D06 sp017540505	79.3219	268	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	98.96	98.96	0.87	0.87	2	-
GCA_017551725.1	s__F23-D06 sp017551725	79.2313	226	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315705.1	s__F23-D06 sp900315705	78.9676	260	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	96.57	95.67	0.83	0.75	8	-
GCA_902786595.1	s__F23-D06 sp902786595	78.6	186	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	96.23	96.23	0.81	0.81	2	-
GCA_002311645.1	s__F23-D06 sp002311645	78.2458	203	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	99.56	99.21	0.92	0.91	3	-
GCA_902770735.1	s__F23-D06 sp902770735	78.2235	170	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	97.49	97.03	0.76	0.71	3	-
GCA_017527945.1	s__F23-D06 sp017527945	78.0138	168	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017633495.1	s__F23-D06 sp017633495	77.7872	139	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:38:08,216] [INFO] GTDB search result was written to GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 10:38:08,216] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:38:08,220] [INFO] DFAST_QC result json was written to GCA_946409355.1_SRR12081296_bin.8_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 10:38:08,220] [INFO] DFAST_QC completed!
[2023-06-30 10:38:08,220] [INFO] Total running time: 0h1m32s