[2023-03-17 11:36:53,945] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:36:53,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:36:53,946] [INFO] DQC Reference Directory: /var/lib/cwl/stga6c0f27d-9f81-4eac-bc31-1f42572b6fa9/dqc_reference
[2023-03-17 11:36:55,036] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:36:55,037] [INFO] Task started: Prodigal
[2023-03-17 11:36:55,037] [INFO] Running command: cat /var/lib/cwl/stgb55528e9-c091-488d-9cce-efd06b96fbcd/OceanDNA-a1740.fa | prodigal -d OceanDNA-a1740/cds.fna -a OceanDNA-a1740/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:37:00,506] [INFO] Task succeeded: Prodigal
[2023-03-17 11:37:00,506] [INFO] Task started: HMMsearch
[2023-03-17 11:37:00,506] [INFO] Running command: hmmsearch --tblout OceanDNA-a1740/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6c0f27d-9f81-4eac-bc31-1f42572b6fa9/dqc_reference/reference_markers.hmm OceanDNA-a1740/protein.faa > /dev/null
[2023-03-17 11:37:00,638] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:37:00,638] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb55528e9-c091-488d-9cce-efd06b96fbcd/OceanDNA-a1740.fa]
[2023-03-17 11:37:00,649] [INFO] Query marker FASTA was written to OceanDNA-a1740/markers.fasta
[2023-03-17 11:37:00,650] [INFO] Task started: Blastn
[2023-03-17 11:37:00,650] [INFO] Running command: blastn -query OceanDNA-a1740/markers.fasta -db /var/lib/cwl/stga6c0f27d-9f81-4eac-bc31-1f42572b6fa9/dqc_reference/reference_markers.fasta -out OceanDNA-a1740/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:01,160] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:01,162] [INFO] Selected 6 target genomes.
[2023-03-17 11:37:01,162] [INFO] Target genome list was writen to OceanDNA-a1740/target_genomes.txt
[2023-03-17 11:37:01,166] [INFO] Task started: fastANI
[2023-03-17 11:37:01,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgb55528e9-c091-488d-9cce-efd06b96fbcd/OceanDNA-a1740.fa --refList OceanDNA-a1740/target_genomes.txt --output OceanDNA-a1740/fastani_result.tsv --threads 1
[2023-03-17 11:37:04,868] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:04,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6c0f27d-9f81-4eac-bc31-1f42572b6fa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:37:04,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6c0f27d-9f81-4eac-bc31-1f42572b6fa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:37:04,869] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:37:04,869] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:37:04,869] [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
--------------------------------------------------------------------------------
[2023-03-17 11:37:04,870] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1740/tc_result.tsv
[2023-03-17 11:37:04,871] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:37:04,871] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:37:04,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6c0f27d-9f81-4eac-bc31-1f42572b6fa9/dqc_reference/checkm_data
[2023-03-17 11:37:04,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:37:05,201] [INFO] Task started: CheckM
[2023-03-17 11:37:05,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1740/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1740/checkm_input OceanDNA-a1740/checkm_result
[2023-03-17 11:37:25,436] [INFO] Task succeeded: CheckM
[2023-03-17 11:37:25,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:37:25,444] [INFO] ===== Completeness check finished =====
[2023-03-17 11:37:25,444] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:37:25,444] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1740/markers.fasta)
[2023-03-17 11:37:25,445] [INFO] Task started: Blastn
[2023-03-17 11:37:25,445] [INFO] Running command: blastn -query OceanDNA-a1740/markers.fasta -db /var/lib/cwl/stga6c0f27d-9f81-4eac-bc31-1f42572b6fa9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1740/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:26,174] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:26,179] [INFO] Selected 7 target genomes.
[2023-03-17 11:37:26,179] [INFO] Target genome list was writen to OceanDNA-a1740/target_genomes_gtdb.txt
[2023-03-17 11:37:26,187] [INFO] Task started: fastANI
[2023-03-17 11:37:26,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgb55528e9-c091-488d-9cce-efd06b96fbcd/OceanDNA-a1740.fa --refList OceanDNA-a1740/target_genomes_gtdb.txt --output OceanDNA-a1740/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:37:28,860] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:28,863] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:37:28,863] [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_003193815.1	s__UBA8886 sp003193815	95.2395	96	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002509165.1	s__UBA8886 sp002509165	90.61	143	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	99.54	99.45	0.84	0.83	3	-
GCA_002731905.1	s__UBA8886 sp002731905	79.9673	91	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:37:28,864] [INFO] GTDB search result was written to OceanDNA-a1740/result_gtdb.tsv
[2023-03-17 11:37:28,865] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:37:28,867] [INFO] DFAST_QC result json was written to OceanDNA-a1740/dqc_result.json
[2023-03-17 11:37:28,867] [INFO] DFAST_QC completed!
[2023-03-17 11:37:28,867] [INFO] Total running time: 0h0m35s