[2023-06-08 04:43:40,462] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:43:40,464] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:43:40,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgff7e4c42-6181-4d4f-aec2-a03e5a155767/dqc_reference
[2023-06-08 04:43:41,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:43:41,690] [INFO] Task started: Prodigal
[2023-06-08 04:43:41,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg766b7caf-7023-4a92-9872-4eae856717c7/GCA_902614205.1_AG-891-K10_genomic.fna.gz | prodigal -d GCA_902614205.1_AG-891-K10_genomic.fna/cds.fna -a GCA_902614205.1_AG-891-K10_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:43:42,423] [INFO] Task succeeded: Prodigal
[2023-06-08 04:43:42,424] [INFO] Task started: HMMsearch
[2023-06-08 04:43:42,424] [INFO] Running command: hmmsearch --tblout GCA_902614205.1_AG-891-K10_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff7e4c42-6181-4d4f-aec2-a03e5a155767/dqc_reference/reference_markers.hmm GCA_902614205.1_AG-891-K10_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:43:42,636] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:43:42,637] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg766b7caf-7023-4a92-9872-4eae856717c7/GCA_902614205.1_AG-891-K10_genomic.fna.gz]
[2023-06-08 04:43:42,655] [INFO] Query marker FASTA was written to GCA_902614205.1_AG-891-K10_genomic.fna/markers.fasta
[2023-06-08 04:43:42,655] [INFO] Task started: Blastn
[2023-06-08 04:43:42,655] [INFO] Running command: blastn -query GCA_902614205.1_AG-891-K10_genomic.fna/markers.fasta -db /var/lib/cwl/stgff7e4c42-6181-4d4f-aec2-a03e5a155767/dqc_reference/reference_markers.fasta -out GCA_902614205.1_AG-891-K10_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:43:43,180] [INFO] Task succeeded: Blastn
[2023-06-08 04:43:43,184] [INFO] Selected 5 target genomes.
[2023-06-08 04:43:43,185] [INFO] Target genome list was writen to GCA_902614205.1_AG-891-K10_genomic.fna/target_genomes.txt
[2023-06-08 04:43:43,187] [INFO] Task started: fastANI
[2023-06-08 04:43:43,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg766b7caf-7023-4a92-9872-4eae856717c7/GCA_902614205.1_AG-891-K10_genomic.fna.gz --refList GCA_902614205.1_AG-891-K10_genomic.fna/target_genomes.txt --output GCA_902614205.1_AG-891-K10_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:43:45,670] [INFO] Task succeeded: fastANI
[2023-06-08 04:43:45,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff7e4c42-6181-4d4f-aec2-a03e5a155767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:43:45,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff7e4c42-6181-4d4f-aec2-a03e5a155767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:43:45,674] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:43:45,674] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 04:43:45,674] [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
--------------------------------------------------------------------------------
[2023-06-08 04:43:45,676] [INFO] DFAST Taxonomy check result was written to GCA_902614205.1_AG-891-K10_genomic.fna/tc_result.tsv
[2023-06-08 04:43:45,676] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:43:45,677] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:43:45,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff7e4c42-6181-4d4f-aec2-a03e5a155767/dqc_reference/checkm_data
[2023-06-08 04:43:45,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:43:45,703] [INFO] Task started: CheckM
[2023-06-08 04:43:45,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614205.1_AG-891-K10_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614205.1_AG-891-K10_genomic.fna/checkm_input GCA_902614205.1_AG-891-K10_genomic.fna/checkm_result
[2023-06-08 04:43:55,926] [INFO] Task succeeded: CheckM
[2023-06-08 04:43:55,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 21.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:43:55,943] [INFO] ===== Completeness check finished =====
[2023-06-08 04:43:55,943] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:43:55,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614205.1_AG-891-K10_genomic.fna/markers.fasta)
[2023-06-08 04:43:55,944] [INFO] Task started: Blastn
[2023-06-08 04:43:55,944] [INFO] Running command: blastn -query GCA_902614205.1_AG-891-K10_genomic.fna/markers.fasta -db /var/lib/cwl/stgff7e4c42-6181-4d4f-aec2-a03e5a155767/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614205.1_AG-891-K10_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:43:56,517] [INFO] Task succeeded: Blastn
[2023-06-08 04:43:56,521] [INFO] Selected 8 target genomes.
[2023-06-08 04:43:56,522] [INFO] Target genome list was writen to GCA_902614205.1_AG-891-K10_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:43:56,525] [INFO] Task started: fastANI
[2023-06-08 04:43:56,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg766b7caf-7023-4a92-9872-4eae856717c7/GCA_902614205.1_AG-891-K10_genomic.fna.gz --refList GCA_902614205.1_AG-891-K10_genomic.fna/target_genomes_gtdb.txt --output GCA_902614205.1_AG-891-K10_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:43:57,977] [INFO] Task succeeded: fastANI
[2023-06-08 04:43:57,985] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 04:43:57,986] [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_902547955.1	s__MED-G10 sp902547955	91.1631	105	132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.61	97.06	0.82	0.80	5	-
GCA_902590895.1	s__MED-G10 sp902590895	89.4037	73	132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712255.1	s__MED-G10 sp002712255	79.7145	61	132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:43:57,988] [INFO] GTDB search result was written to GCA_902614205.1_AG-891-K10_genomic.fna/result_gtdb.tsv
[2023-06-08 04:43:57,989] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:43:57,991] [INFO] DFAST_QC result json was written to GCA_902614205.1_AG-891-K10_genomic.fna/dqc_result.json
[2023-06-08 04:43:57,991] [INFO] DFAST_QC completed!
[2023-06-08 04:43:57,991] [INFO] Total running time: 0h0m18s