[2023-06-04 19:29:30,807] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:29:30,810] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:29:30,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc0e086e-cbe3-460b-bb2d-16f198aa42cc/dqc_reference
[2023-06-04 19:29:32,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:29:32,005] [INFO] Task started: Prodigal
[2023-06-04 19:29:32,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg6917d34e-06df-4067-8e9c-613fa0899332/GCA_934087285.1_ERR7738593_bin.196_genomic.fna.gz | prodigal -d GCA_934087285.1_ERR7738593_bin.196_genomic.fna/cds.fna -a GCA_934087285.1_ERR7738593_bin.196_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:29:38,578] [INFO] Task succeeded: Prodigal
[2023-06-04 19:29:38,578] [INFO] Task started: HMMsearch
[2023-06-04 19:29:38,579] [INFO] Running command: hmmsearch --tblout GCA_934087285.1_ERR7738593_bin.196_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc0e086e-cbe3-460b-bb2d-16f198aa42cc/dqc_reference/reference_markers.hmm GCA_934087285.1_ERR7738593_bin.196_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:29:38,830] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:29:38,832] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6917d34e-06df-4067-8e9c-613fa0899332/GCA_934087285.1_ERR7738593_bin.196_genomic.fna.gz]
[2023-06-04 19:29:38,874] [INFO] Query marker FASTA was written to GCA_934087285.1_ERR7738593_bin.196_genomic.fna/markers.fasta
[2023-06-04 19:29:38,874] [INFO] Task started: Blastn
[2023-06-04 19:29:38,874] [INFO] Running command: blastn -query GCA_934087285.1_ERR7738593_bin.196_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc0e086e-cbe3-460b-bb2d-16f198aa42cc/dqc_reference/reference_markers.fasta -out GCA_934087285.1_ERR7738593_bin.196_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:29:39,398] [INFO] Task succeeded: Blastn
[2023-06-04 19:29:39,403] [INFO] Selected 10 target genomes.
[2023-06-04 19:29:39,404] [INFO] Target genome list was writen to GCA_934087285.1_ERR7738593_bin.196_genomic.fna/target_genomes.txt
[2023-06-04 19:29:39,406] [INFO] Task started: fastANI
[2023-06-04 19:29:39,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg6917d34e-06df-4067-8e9c-613fa0899332/GCA_934087285.1_ERR7738593_bin.196_genomic.fna.gz --refList GCA_934087285.1_ERR7738593_bin.196_genomic.fna/target_genomes.txt --output GCA_934087285.1_ERR7738593_bin.196_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:29:42,300] [INFO] Task succeeded: fastANI
[2023-06-04 19:29:42,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc0e086e-cbe3-460b-bb2d-16f198aa42cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:29:42,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc0e086e-cbe3-460b-bb2d-16f198aa42cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:29:42,303] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:29:42,304] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:29:42,304] [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
--------------------------------------------------------------------------------
[2023-06-04 19:29:42,307] [INFO] DFAST Taxonomy check result was written to GCA_934087285.1_ERR7738593_bin.196_genomic.fna/tc_result.tsv
[2023-06-04 19:29:42,307] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:29:42,308] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:29:42,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc0e086e-cbe3-460b-bb2d-16f198aa42cc/dqc_reference/checkm_data
[2023-06-04 19:29:42,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:29:42,360] [INFO] Task started: CheckM
[2023-06-04 19:29:42,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934087285.1_ERR7738593_bin.196_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934087285.1_ERR7738593_bin.196_genomic.fna/checkm_input GCA_934087285.1_ERR7738593_bin.196_genomic.fna/checkm_result
[2023-06-04 19:30:08,312] [INFO] Task succeeded: CheckM
[2023-06-04 19:30:08,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.89%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:30:08,340] [INFO] ===== Completeness check finished =====
[2023-06-04 19:30:08,340] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:30:08,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934087285.1_ERR7738593_bin.196_genomic.fna/markers.fasta)
[2023-06-04 19:30:08,341] [INFO] Task started: Blastn
[2023-06-04 19:30:08,341] [INFO] Running command: blastn -query GCA_934087285.1_ERR7738593_bin.196_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc0e086e-cbe3-460b-bb2d-16f198aa42cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934087285.1_ERR7738593_bin.196_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:30:08,922] [INFO] Task succeeded: Blastn
[2023-06-04 19:30:08,926] [INFO] Selected 7 target genomes.
[2023-06-04 19:30:08,926] [INFO] Target genome list was writen to GCA_934087285.1_ERR7738593_bin.196_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:30:08,971] [INFO] Task started: fastANI
[2023-06-04 19:30:08,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg6917d34e-06df-4067-8e9c-613fa0899332/GCA_934087285.1_ERR7738593_bin.196_genomic.fna.gz --refList GCA_934087285.1_ERR7738593_bin.196_genomic.fna/target_genomes_gtdb.txt --output GCA_934087285.1_ERR7738593_bin.196_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:30:10,345] [INFO] Task succeeded: fastANI
[2023-06-04 19:30:10,352] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:30:10,352] [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_900548725.1	s__UMGS1124 sp900548725	95.1822	107	582	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1124	95.0	99.98	99.98	0.92	0.92	2	conclusive
GCA_017411405.1	s__UMGS1124 sp017411405	78.2953	74	582	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1124	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:30:10,354] [INFO] GTDB search result was written to GCA_934087285.1_ERR7738593_bin.196_genomic.fna/result_gtdb.tsv
[2023-06-04 19:30:10,355] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:30:10,357] [INFO] DFAST_QC result json was written to GCA_934087285.1_ERR7738593_bin.196_genomic.fna/dqc_result.json
[2023-06-04 19:30:10,357] [INFO] DFAST_QC completed!
[2023-06-04 19:30:10,358] [INFO] Total running time: 0h0m40s