[2023-06-16 21:48:18,161] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:48:18,163] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:48:18,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg7328a1e5-3571-4b91-b001-6b230ce03b02/dqc_reference
[2023-06-16 21:48:19,434] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:48:19,435] [INFO] Task started: Prodigal
[2023-06-16 21:48:19,435] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a1ac9aa-ea04-4685-b8a1-a1bfdadbcc3b/GCA_028820765.1_ASM2882076v1_genomic.fna.gz | prodigal -d GCA_028820765.1_ASM2882076v1_genomic.fna/cds.fna -a GCA_028820765.1_ASM2882076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:48:26,778] [INFO] Task succeeded: Prodigal
[2023-06-16 21:48:26,778] [INFO] Task started: HMMsearch
[2023-06-16 21:48:26,778] [INFO] Running command: hmmsearch --tblout GCA_028820765.1_ASM2882076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7328a1e5-3571-4b91-b001-6b230ce03b02/dqc_reference/reference_markers.hmm GCA_028820765.1_ASM2882076v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:48:27,101] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:48:27,103] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1a1ac9aa-ea04-4685-b8a1-a1bfdadbcc3b/GCA_028820765.1_ASM2882076v1_genomic.fna.gz]
[2023-06-16 21:48:27,138] [INFO] Query marker FASTA was written to GCA_028820765.1_ASM2882076v1_genomic.fna/markers.fasta
[2023-06-16 21:48:27,139] [INFO] Task started: Blastn
[2023-06-16 21:48:27,139] [INFO] Running command: blastn -query GCA_028820765.1_ASM2882076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7328a1e5-3571-4b91-b001-6b230ce03b02/dqc_reference/reference_markers.fasta -out GCA_028820765.1_ASM2882076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:48:27,717] [INFO] Task succeeded: Blastn
[2023-06-16 21:48:27,721] [INFO] Selected 5 target genomes.
[2023-06-16 21:48:27,722] [INFO] Target genome list was writen to GCA_028820765.1_ASM2882076v1_genomic.fna/target_genomes.txt
[2023-06-16 21:48:27,724] [INFO] Task started: fastANI
[2023-06-16 21:48:27,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1ac9aa-ea04-4685-b8a1-a1bfdadbcc3b/GCA_028820765.1_ASM2882076v1_genomic.fna.gz --refList GCA_028820765.1_ASM2882076v1_genomic.fna/target_genomes.txt --output GCA_028820765.1_ASM2882076v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:48:30,705] [INFO] Task succeeded: fastANI
[2023-06-16 21:48:30,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7328a1e5-3571-4b91-b001-6b230ce03b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:48:30,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7328a1e5-3571-4b91-b001-6b230ce03b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:48:30,709] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:48:30,709] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 21:48:30,709] [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
--------------------------------------------------------------------------------
[2023-06-16 21:48:30,711] [INFO] DFAST Taxonomy check result was written to GCA_028820765.1_ASM2882076v1_genomic.fna/tc_result.tsv
[2023-06-16 21:48:30,711] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:48:30,711] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:48:30,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7328a1e5-3571-4b91-b001-6b230ce03b02/dqc_reference/checkm_data
[2023-06-16 21:48:30,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:48:30,750] [INFO] Task started: CheckM
[2023-06-16 21:48:30,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028820765.1_ASM2882076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028820765.1_ASM2882076v1_genomic.fna/checkm_input GCA_028820765.1_ASM2882076v1_genomic.fna/checkm_result
[2023-06-16 21:48:58,128] [INFO] Task succeeded: CheckM
[2023-06-16 21:48:58,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:48:58,148] [INFO] ===== Completeness check finished =====
[2023-06-16 21:48:58,149] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:48:58,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028820765.1_ASM2882076v1_genomic.fna/markers.fasta)
[2023-06-16 21:48:58,150] [INFO] Task started: Blastn
[2023-06-16 21:48:58,150] [INFO] Running command: blastn -query GCA_028820765.1_ASM2882076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7328a1e5-3571-4b91-b001-6b230ce03b02/dqc_reference/reference_markers_gtdb.fasta -out GCA_028820765.1_ASM2882076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:48:58,879] [INFO] Task succeeded: Blastn
[2023-06-16 21:48:58,888] [INFO] Selected 7 target genomes.
[2023-06-16 21:48:58,889] [INFO] Target genome list was writen to GCA_028820765.1_ASM2882076v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:48:58,890] [INFO] Task started: fastANI
[2023-06-16 21:48:58,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1ac9aa-ea04-4685-b8a1-a1bfdadbcc3b/GCA_028820765.1_ASM2882076v1_genomic.fna.gz --refList GCA_028820765.1_ASM2882076v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028820765.1_ASM2882076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:49:05,265] [INFO] Task succeeded: fastANI
[2023-06-16 21:49:05,277] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 21:49:05,278] [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_011523365.1	s__Bin5 sp011523365	85.7893	588	787	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840225.1	s__Bin5 sp009840225	85.0583	554	787	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	97.63	95.35	0.89	0.84	3	-
GCA_009841235.1	s__Bin5 sp009841235	82.6889	512	787	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	95.53	95.53	0.91	0.91	2	-
GCA_009838625.1	s__Bin5 sp009838625	81.3676	471	787	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	99.90	99.90	0.97	0.97	2	-
GCA_002238445.1	s__Bin5 sp002238445	79.2347	357	787	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 21:49:05,281] [INFO] GTDB search result was written to GCA_028820765.1_ASM2882076v1_genomic.fna/result_gtdb.tsv
[2023-06-16 21:49:05,282] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:49:05,286] [INFO] DFAST_QC result json was written to GCA_028820765.1_ASM2882076v1_genomic.fna/dqc_result.json
[2023-06-16 21:49:05,286] [INFO] DFAST_QC completed!
[2023-06-16 21:49:05,286] [INFO] Total running time: 0h0m47s