[2023-06-30 17:54:07,661] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:54:07,663] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:54:07,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f4d21a7-fc9d-4298-8035-8b0bee1231c6/dqc_reference
[2023-06-30 17:54:08,911] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:54:08,912] [INFO] Task started: Prodigal
[2023-06-30 17:54:08,913] [INFO] Running command: gunzip -c /var/lib/cwl/stgd492dc8f-505d-4d60-897d-6b22eb8dd492/GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:54:11,229] [INFO] Task succeeded: Prodigal
[2023-06-30 17:54:11,229] [INFO] Task started: HMMsearch
[2023-06-30 17:54:11,230] [INFO] Running command: hmmsearch --tblout GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f4d21a7-fc9d-4298-8035-8b0bee1231c6/dqc_reference/reference_markers.hmm GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:54:11,437] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:54:11,439] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd492dc8f-505d-4d60-897d-6b22eb8dd492/GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-30 17:54:11,460] [INFO] Query marker FASTA was written to GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 17:54:11,460] [INFO] Task started: Blastn
[2023-06-30 17:54:11,460] [INFO] Running command: blastn -query GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f4d21a7-fc9d-4298-8035-8b0bee1231c6/dqc_reference/reference_markers.fasta -out GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:54:12,015] [INFO] Task succeeded: Blastn
[2023-06-30 17:54:12,020] [INFO] Selected 19 target genomes.
[2023-06-30 17:54:12,020] [INFO] Target genome list was writen to GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 17:54:12,028] [INFO] Task started: fastANI
[2023-06-30 17:54:12,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgd492dc8f-505d-4d60-897d-6b22eb8dd492/GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:54:18,379] [INFO] Task succeeded: fastANI
[2023-06-30 17:54:18,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f4d21a7-fc9d-4298-8035-8b0bee1231c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:54:18,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f4d21a7-fc9d-4298-8035-8b0bee1231c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:54:18,382] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:54:18,382] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 17:54:18,382] [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 17:54:18,384] [INFO] DFAST Taxonomy check result was written to GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 17:54:18,385] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:54:18,385] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:54:18,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f4d21a7-fc9d-4298-8035-8b0bee1231c6/dqc_reference/checkm_data
[2023-06-30 17:54:18,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:54:18,407] [INFO] Task started: CheckM
[2023-06-30 17:54:18,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 17:54:33,774] [INFO] Task succeeded: CheckM
[2023-06-30 17:54:33,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:54:33,796] [INFO] ===== Completeness check finished =====
[2023-06-30 17:54:33,797] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:54:33,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 17:54:33,798] [INFO] Task started: Blastn
[2023-06-30 17:54:33,798] [INFO] Running command: blastn -query GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f4d21a7-fc9d-4298-8035-8b0bee1231c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:54:34,599] [INFO] Task succeeded: Blastn
[2023-06-30 17:54:34,604] [INFO] Selected 16 target genomes.
[2023-06-30 17:54:34,605] [INFO] Target genome list was writen to GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:54:34,620] [INFO] Task started: fastANI
[2023-06-30 17:54:34,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgd492dc8f-505d-4d60-897d-6b22eb8dd492/GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:54:38,564] [INFO] Task succeeded: fastANI
[2023-06-30 17:54:38,591] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 17:54:38,591] [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_902780395.1	s__UBA3789 sp902780395	78.8777	176	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782835.1	s__UBA3789 sp902782835	78.6065	152	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780585.1	s__UBA3789 sp902780585	78.5647	141	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.24	98.24	0.79	0.79	2	-
GCA_002369415.1	s__UBA3789 sp002369415	78.2591	135	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797265.1	s__UBA3789 sp902797265	78.2526	143	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432645.1	s__UBA3789 sp017432645	78.2162	109	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432665.1	s__UBA3789 sp017432665	78.2143	105	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017964405.1	s__UBA3789 sp017964405	78.1772	147	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405445.1	s__UBA3789 sp017405445	78.0917	159	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541885.1	s__UBA3789 sp017541885	78.0888	159	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017511375.1	s__UBA3789 sp017511375	78.0448	126	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783435.1	s__UBA3789 sp902783435	78.0115	143	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796215.1	s__UBA3789 sp902796215	77.9736	120	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017511605.1	s__UBA3789 sp017511605	77.899	94	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783315.1	s__UBA3789 sp902783315	77.81	110	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767005.1	s__RUG11224 sp902767005	77.0878	73	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11224	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:54:38,594] [INFO] GTDB search result was written to GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 17:54:38,594] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:54:38,598] [INFO] DFAST_QC result json was written to GCA_946539445.1_SRR873596_bin.89_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 17:54:38,599] [INFO] DFAST_QC completed!
[2023-06-30 17:54:38,599] [INFO] Total running time: 0h0m31s