[2023-06-28 12:28:04,405] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:28:04,412] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:28:04,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg443b700f-72cf-4d41-b856-15b135a3b903/dqc_reference
[2023-06-28 12:28:06,029] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:28:06,030] [INFO] Task started: Prodigal
[2023-06-28 12:28:06,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg31f72ada-9868-4c14-9928-638c797788b5/GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:28:12,314] [INFO] Task succeeded: Prodigal
[2023-06-28 12:28:12,314] [INFO] Task started: HMMsearch
[2023-06-28 12:28:12,314] [INFO] Running command: hmmsearch --tblout GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg443b700f-72cf-4d41-b856-15b135a3b903/dqc_reference/reference_markers.hmm GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:28:12,548] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:28:12,550] [INFO] Found 6/6 markers.
[2023-06-28 12:28:12,575] [INFO] Query marker FASTA was written to GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 12:28:12,575] [INFO] Task started: Blastn
[2023-06-28 12:28:12,576] [INFO] Running command: blastn -query GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg443b700f-72cf-4d41-b856-15b135a3b903/dqc_reference/reference_markers.fasta -out GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:28:13,156] [INFO] Task succeeded: Blastn
[2023-06-28 12:28:13,160] [INFO] Selected 19 target genomes.
[2023-06-28 12:28:13,160] [INFO] Target genome list was writen to GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 12:28:13,162] [INFO] Task started: fastANI
[2023-06-28 12:28:13,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f72ada-9868-4c14-9928-638c797788b5/GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:28:20,455] [INFO] Task succeeded: fastANI
[2023-06-28 12:28:20,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg443b700f-72cf-4d41-b856-15b135a3b903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:28:20,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg443b700f-72cf-4d41-b856-15b135a3b903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:28:20,458] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:28:20,458] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:28:20,459] [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
--------------------------------------------------------------------------------
[2023-06-28 12:28:20,461] [INFO] DFAST Taxonomy check result was written to GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 12:28:20,462] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:28:20,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:28:20,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg443b700f-72cf-4d41-b856-15b135a3b903/dqc_reference/checkm_data
[2023-06-28 12:28:20,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:28:20,495] [INFO] Task started: CheckM
[2023-06-28 12:28:20,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 12:28:45,449] [INFO] Task succeeded: CheckM
[2023-06-28 12:28:45,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:28:45,476] [INFO] ===== Completeness check finished =====
[2023-06-28 12:28:45,476] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:28:45,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 12:28:45,477] [INFO] Task started: Blastn
[2023-06-28 12:28:45,477] [INFO] Running command: blastn -query GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg443b700f-72cf-4d41-b856-15b135a3b903/dqc_reference/reference_markers_gtdb.fasta -out GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:28:46,262] [INFO] Task succeeded: Blastn
[2023-06-28 12:28:46,267] [INFO] Selected 14 target genomes.
[2023-06-28 12:28:46,267] [INFO] Target genome list was writen to GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:28:46,282] [INFO] Task started: fastANI
[2023-06-28 12:28:46,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f72ada-9868-4c14-9928-638c797788b5/GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:28:52,965] [INFO] Task succeeded: fastANI
[2023-06-28 12:28:52,976] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:28:52,976] [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_003612515.1	s__D16-34 sp003612515	99.1125	662	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-34	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910588485.1	s__D16-34 sp910588485	81.5184	390	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577495.1	s__D16-34 sp910577495	80.8837	356	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340345.1	s__Paraeggerthella hongkongensis_A	76.7561	57	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella	95.0	98.75	98.26	0.95	0.89	5	-
GCF_000270285.1	s__Enteroscipio sp000270285	76.61	57	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Enteroscipio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:28:52,979] [INFO] GTDB search result was written to GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 12:28:52,980] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:28:52,983] [INFO] DFAST_QC result json was written to GCA_948435005.1_SRR15730533_bin.66_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 12:28:52,983] [INFO] DFAST_QC completed!
[2023-06-28 12:28:52,983] [INFO] Total running time: 0h0m49s