[2023-03-18 23:56:04,497] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:56:04,498] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:56:04,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7110983-c140-4369-ba4d-3701117e30d1/dqc_reference
[2023-03-18 23:56:05,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:56:05,621] [INFO] Task started: Prodigal
[2023-03-18 23:56:05,621] [INFO] Running command: cat /var/lib/cwl/stg8f537470-098e-4d90-a4df-a88ceab264d5/OceanDNA-b1936.fa | prodigal -d OceanDNA-b1936/cds.fna -a OceanDNA-b1936/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:56:08,248] [INFO] Task succeeded: Prodigal
[2023-03-18 23:56:08,248] [INFO] Task started: HMMsearch
[2023-03-18 23:56:08,248] [INFO] Running command: hmmsearch --tblout OceanDNA-b1936/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7110983-c140-4369-ba4d-3701117e30d1/dqc_reference/reference_markers.hmm OceanDNA-b1936/protein.faa > /dev/null
[2023-03-18 23:56:08,355] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:56:08,356] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8f537470-098e-4d90-a4df-a88ceab264d5/OceanDNA-b1936.fa]
[2023-03-18 23:56:08,361] [INFO] Query marker FASTA was written to OceanDNA-b1936/markers.fasta
[2023-03-18 23:56:08,363] [INFO] Task started: Blastn
[2023-03-18 23:56:08,363] [INFO] Running command: blastn -query OceanDNA-b1936/markers.fasta -db /var/lib/cwl/stgb7110983-c140-4369-ba4d-3701117e30d1/dqc_reference/reference_markers.fasta -out OceanDNA-b1936/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:08,890] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:08,891] [INFO] Selected 5 target genomes.
[2023-03-18 23:56:08,891] [INFO] Target genome list was writen to OceanDNA-b1936/target_genomes.txt
[2023-03-18 23:56:08,895] [INFO] Task started: fastANI
[2023-03-18 23:56:08,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f537470-098e-4d90-a4df-a88ceab264d5/OceanDNA-b1936.fa --refList OceanDNA-b1936/target_genomes.txt --output OceanDNA-b1936/fastani_result.tsv --threads 1
[2023-03-18 23:56:11,648] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:11,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7110983-c140-4369-ba4d-3701117e30d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:56:11,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7110983-c140-4369-ba4d-3701117e30d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:56:11,648] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:56:11,648] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:56:11,648] [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
--------------------------------------------------------------------------------
[2023-03-18 23:56:11,649] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1936/tc_result.tsv
[2023-03-18 23:56:11,649] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:56:11,649] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:56:11,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7110983-c140-4369-ba4d-3701117e30d1/dqc_reference/checkm_data
[2023-03-18 23:56:11,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:56:11,655] [INFO] Task started: CheckM
[2023-03-18 23:56:11,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1936/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1936/checkm_input OceanDNA-b1936/checkm_result
[2023-03-18 23:56:24,636] [INFO] Task succeeded: CheckM
[2023-03-18 23:56:24,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:56:24,638] [INFO] ===== Completeness check finished =====
[2023-03-18 23:56:24,638] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:56:24,638] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1936/markers.fasta)
[2023-03-18 23:56:24,638] [INFO] Task started: Blastn
[2023-03-18 23:56:24,638] [INFO] Running command: blastn -query OceanDNA-b1936/markers.fasta -db /var/lib/cwl/stgb7110983-c140-4369-ba4d-3701117e30d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1936/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:25,280] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:25,281] [INFO] Selected 12 target genomes.
[2023-03-18 23:56:25,281] [INFO] Target genome list was writen to OceanDNA-b1936/target_genomes_gtdb.txt
[2023-03-18 23:56:25,295] [INFO] Task started: fastANI
[2023-03-18 23:56:25,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f537470-098e-4d90-a4df-a88ceab264d5/OceanDNA-b1936.fa --refList OceanDNA-b1936/target_genomes_gtdb.txt --output OceanDNA-b1936/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:56:28,100] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:28,104] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:56:28,104] [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_002712325.1	s__UBA8592 sp002712325	99.2205	142	155	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.19	99.19	0.77	0.77	2	conclusive
GCA_002713605.1	s__UBA8592 sp002713605	81.7961	60	155	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.46	99.46	0.60	0.60	2	-
GCA_002295705.1	s__UBA8592 sp002295705	81.5296	108	155	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.20	99.08	0.80	0.73	4	-
GCA_011523005.1	s__UBA8592 sp002380145	80.7163	116	155	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.37	95.83	0.82	0.81	6	-
GCA_002712415.1	s__UBA8592 sp002712415	79.9347	100	155	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.66	97.33	0.73	0.67	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:56:28,104] [INFO] GTDB search result was written to OceanDNA-b1936/result_gtdb.tsv
[2023-03-18 23:56:28,105] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:56:28,105] [INFO] DFAST_QC result json was written to OceanDNA-b1936/dqc_result.json
[2023-03-18 23:56:28,106] [INFO] DFAST_QC completed!
[2023-03-18 23:56:28,106] [INFO] Total running time: 0h0m24s