[2023-06-30 00:38:45,074] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:38:45,096] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:38:45,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg12ba2b4a-ddcc-4087-b8e8-a8c3e63af70a/dqc_reference
[2023-06-30 00:38:46,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:38:46,311] [INFO] Task started: Prodigal
[2023-06-30 00:38:46,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg47f7c1b5-13b1-42b4-b54f-87f8b0bfa265/GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna.gz | prodigal -d GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/cds.fna -a GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:38:47,204] [INFO] Task succeeded: Prodigal
[2023-06-30 00:38:47,204] [INFO] Task started: HMMsearch
[2023-06-30 00:38:47,204] [INFO] Running command: hmmsearch --tblout GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12ba2b4a-ddcc-4087-b8e8-a8c3e63af70a/dqc_reference/reference_markers.hmm GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:38:47,411] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:38:47,412] [INFO] Found 6/6 markers.
[2023-06-30 00:38:47,434] [INFO] Query marker FASTA was written to GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/markers.fasta
[2023-06-30 00:38:47,434] [INFO] Task started: Blastn
[2023-06-30 00:38:47,435] [INFO] Running command: blastn -query GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/markers.fasta -db /var/lib/cwl/stg12ba2b4a-ddcc-4087-b8e8-a8c3e63af70a/dqc_reference/reference_markers.fasta -out GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:38:49,489] [INFO] Task succeeded: Blastn
[2023-06-30 00:38:49,493] [INFO] Selected 9 target genomes.
[2023-06-30 00:38:49,493] [INFO] Target genome list was writen to GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/target_genomes.txt
[2023-06-30 00:38:49,495] [INFO] Task started: fastANI
[2023-06-30 00:38:49,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f7c1b5-13b1-42b4-b54f-87f8b0bfa265/GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna.gz --refList GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/target_genomes.txt --output GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:38:55,048] [INFO] Task succeeded: fastANI
[2023-06-30 00:38:55,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12ba2b4a-ddcc-4087-b8e8-a8c3e63af70a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:38:55,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12ba2b4a-ddcc-4087-b8e8-a8c3e63af70a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:38:55,050] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:38:55,050] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:38:55,050] [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 00:38:55,052] [INFO] DFAST Taxonomy check result was written to GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/tc_result.tsv
[2023-06-30 00:38:55,053] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:38:55,053] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:38:55,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12ba2b4a-ddcc-4087-b8e8-a8c3e63af70a/dqc_reference/checkm_data
[2023-06-30 00:38:55,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:38:55,065] [INFO] Task started: CheckM
[2023-06-30 00:38:55,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/checkm_input GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/checkm_result
[2023-06-30 00:39:06,002] [INFO] Task succeeded: CheckM
[2023-06-30 00:39:06,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:39:06,019] [INFO] ===== Completeness check finished =====
[2023-06-30 00:39:06,019] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:39:06,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/markers.fasta)
[2023-06-30 00:39:06,020] [INFO] Task started: Blastn
[2023-06-30 00:39:06,020] [INFO] Running command: blastn -query GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/markers.fasta -db /var/lib/cwl/stg12ba2b4a-ddcc-4087-b8e8-a8c3e63af70a/dqc_reference/reference_markers_gtdb.fasta -out GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:39:06,783] [INFO] Task succeeded: Blastn
[2023-06-30 00:39:06,787] [INFO] Selected 23 target genomes.
[2023-06-30 00:39:06,787] [INFO] Target genome list was writen to GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:39:06,801] [INFO] Task started: fastANI
[2023-06-30 00:39:06,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f7c1b5-13b1-42b4-b54f-87f8b0bfa265/GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna.gz --refList GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/target_genomes_gtdb.txt --output GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:39:14,062] [INFO] Task succeeded: fastANI
[2023-06-30 00:39:14,065] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:39:14,065] [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_903840315.1	s__CAIYEO01 sp903840315	86.3086	108	131	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA4665;g__CAIYEO01	95.0	99.98	99.91	0.97	0.90	10	-
--------------------------------------------------------------------------------
[2023-06-30 00:39:14,067] [INFO] GTDB search result was written to GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/result_gtdb.tsv
[2023-06-30 00:39:14,068] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:39:14,070] [INFO] DFAST_QC result json was written to GCA_903839435.1_freshwater_MAG_---_Kiruna_bin-08663_genomic.fna/dqc_result.json
[2023-06-30 00:39:14,071] [INFO] DFAST_QC completed!
[2023-06-30 00:39:14,071] [INFO] Total running time: 0h0m29s