[2023-06-30 21:26:18,544] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:26:18,546] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:26:18,546] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1c94e35-be92-4b07-83ed-3c98d29b0f2e/dqc_reference
[2023-06-30 21:26:19,792] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:26:19,793] [INFO] Task started: Prodigal
[2023-06-30 21:26:19,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c5bcdd0-bf77-4f6f-89b5-782fd9d6e7b6/GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna.gz | prodigal -d GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/cds.fna -a GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:26:22,728] [INFO] Task succeeded: Prodigal
[2023-06-30 21:26:22,729] [INFO] Task started: HMMsearch
[2023-06-30 21:26:22,729] [INFO] Running command: hmmsearch --tblout GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1c94e35-be92-4b07-83ed-3c98d29b0f2e/dqc_reference/reference_markers.hmm GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:26:22,870] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:26:22,871] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4c5bcdd0-bf77-4f6f-89b5-782fd9d6e7b6/GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna.gz]
[2023-06-30 21:26:22,893] [INFO] Query marker FASTA was written to GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/markers.fasta
[2023-06-30 21:26:22,894] [INFO] Task started: Blastn
[2023-06-30 21:26:22,894] [INFO] Running command: blastn -query GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1c94e35-be92-4b07-83ed-3c98d29b0f2e/dqc_reference/reference_markers.fasta -out GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:26:23,446] [INFO] Task succeeded: Blastn
[2023-06-30 21:26:23,450] [INFO] Selected 8 target genomes.
[2023-06-30 21:26:23,451] [INFO] Target genome list was writen to GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/target_genomes.txt
[2023-06-30 21:26:23,451] [INFO] Task started: fastANI
[2023-06-30 21:26:23,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c5bcdd0-bf77-4f6f-89b5-782fd9d6e7b6/GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna.gz --refList GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/target_genomes.txt --output GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:26:27,533] [INFO] Task succeeded: fastANI
[2023-06-30 21:26:27,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1c94e35-be92-4b07-83ed-3c98d29b0f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:26:27,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1c94e35-be92-4b07-83ed-3c98d29b0f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:26:27,536] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:26:27,536] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:26:27,536] [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 21:26:27,538] [INFO] DFAST Taxonomy check result was written to GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/tc_result.tsv
[2023-06-30 21:26:27,539] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:26:27,539] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:26:27,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1c94e35-be92-4b07-83ed-3c98d29b0f2e/dqc_reference/checkm_data
[2023-06-30 21:26:27,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:26:27,613] [INFO] Task started: CheckM
[2023-06-30 21:26:27,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/checkm_input GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/checkm_result
[2023-06-30 21:26:43,380] [INFO] Task succeeded: CheckM
[2023-06-30 21:26:43,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:26:43,399] [INFO] ===== Completeness check finished =====
[2023-06-30 21:26:43,400] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:26:43,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/markers.fasta)
[2023-06-30 21:26:43,400] [INFO] Task started: Blastn
[2023-06-30 21:26:43,400] [INFO] Running command: blastn -query GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1c94e35-be92-4b07-83ed-3c98d29b0f2e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:26:44,171] [INFO] Task succeeded: Blastn
[2023-06-30 21:26:44,175] [INFO] Selected 17 target genomes.
[2023-06-30 21:26:44,176] [INFO] Target genome list was writen to GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:26:44,177] [INFO] Task started: fastANI
[2023-06-30 21:26:44,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c5bcdd0-bf77-4f6f-89b5-782fd9d6e7b6/GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna.gz --refList GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/target_genomes_gtdb.txt --output GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:26:49,501] [INFO] Task succeeded: fastANI
[2023-06-30 21:26:49,506] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:26:49,506] [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_903830745.1	s__RAAP-2 sp903830745	97.4466	210	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	98.28	97.60	0.76	0.72	13	conclusive
GCA_903826715.1	s__RAAP-2 sp903826715	89.8348	198	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.38	98.91	0.84	0.76	7	-
GCA_903854175.1	s__RAAP-2 sp903854175	81.5537	163	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	98.48	97.86	0.79	0.78	3	-
--------------------------------------------------------------------------------
[2023-06-30 21:26:49,508] [INFO] GTDB search result was written to GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/result_gtdb.tsv
[2023-06-30 21:26:49,509] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:26:49,511] [INFO] DFAST_QC result json was written to GCA_903849025.1_freshwater_MAG_---_LinL4_bin-0667_genomic.fna/dqc_result.json
[2023-06-30 21:26:49,512] [INFO] DFAST_QC completed!
[2023-06-30 21:26:49,512] [INFO] Total running time: 0h0m31s