[2023-03-15 21:01:44,325] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,326] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ad54738-ad41-40ac-b6e4-b8e148574b02/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,701] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,702] [INFO] Running command: cat /var/lib/cwl/stg32386deb-80c0-4436-accb-33675f7ae33b/OceanDNA-b5215.fa | prodigal -d OceanDNA-b5215/cds.fna -a OceanDNA-b5215/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:50,947] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:50,947] [INFO] Task started: HMMsearch
[2023-03-15 21:01:50,947] [INFO] Running command: hmmsearch --tblout OceanDNA-b5215/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ad54738-ad41-40ac-b6e4-b8e148574b02/dqc_reference/reference_markers.hmm OceanDNA-b5215/protein.faa > /dev/null
[2023-03-15 21:01:51,085] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:51,086] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32386deb-80c0-4436-accb-33675f7ae33b/OceanDNA-b5215.fa]
[2023-03-15 21:01:51,097] [INFO] Query marker FASTA was written to OceanDNA-b5215/markers.fasta
[2023-03-15 21:01:51,097] [INFO] Task started: Blastn
[2023-03-15 21:01:51,097] [INFO] Running command: blastn -query OceanDNA-b5215/markers.fasta -db /var/lib/cwl/stg3ad54738-ad41-40ac-b6e4-b8e148574b02/dqc_reference/reference_markers.fasta -out OceanDNA-b5215/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:51,615] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:51,616] [INFO] Selected 30 target genomes.
[2023-03-15 21:01:51,616] [INFO] Target genome list was writen to OceanDNA-b5215/target_genomes.txt
[2023-03-15 21:01:51,630] [INFO] Task started: fastANI
[2023-03-15 21:01:51,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg32386deb-80c0-4436-accb-33675f7ae33b/OceanDNA-b5215.fa --refList OceanDNA-b5215/target_genomes.txt --output OceanDNA-b5215/fastani_result.tsv --threads 1
[2023-03-15 21:02:08,325] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:08,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ad54738-ad41-40ac-b6e4-b8e148574b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:08,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ad54738-ad41-40ac-b6e4-b8e148574b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:08,326] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:08,326] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:02:08,326] [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
--------------------------------------------------------------------------------
[2023-03-15 21:02:08,326] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5215/tc_result.tsv
[2023-03-15 21:02:08,326] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:08,326] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:08,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ad54738-ad41-40ac-b6e4-b8e148574b02/dqc_reference/checkm_data
[2023-03-15 21:02:08,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:08,331] [INFO] Task started: CheckM
[2023-03-15 21:02:08,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5215/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5215/checkm_input OceanDNA-b5215/checkm_result
[2023-03-15 21:02:27,873] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:27,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.03%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:27,875] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:27,875] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:27,875] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5215/markers.fasta)
[2023-03-15 21:02:27,876] [INFO] Task started: Blastn
[2023-03-15 21:02:27,876] [INFO] Running command: blastn -query OceanDNA-b5215/markers.fasta -db /var/lib/cwl/stg3ad54738-ad41-40ac-b6e4-b8e148574b02/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5215/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:28,610] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:28,611] [INFO] Selected 20 target genomes.
[2023-03-15 21:02:28,611] [INFO] Target genome list was writen to OceanDNA-b5215/target_genomes_gtdb.txt
[2023-03-15 21:02:29,059] [INFO] Task started: fastANI
[2023-03-15 21:02:29,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg32386deb-80c0-4436-accb-33675f7ae33b/OceanDNA-b5215.fa --refList OceanDNA-b5215/target_genomes_gtdb.txt --output OceanDNA-b5215/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:37,514] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:37,517] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:02:37,517] [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_003454845.1	s__UBA8444 sp003454845	89.19	79	163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779995.1	s__UBA8444 sp016779995	88.8242	152	163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714805.1	s__UBA8444 sp002714805	84.0551	115	163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	95.59	95.59	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:02:37,517] [INFO] GTDB search result was written to OceanDNA-b5215/result_gtdb.tsv
[2023-03-15 21:02:37,518] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:37,518] [INFO] DFAST_QC result json was written to OceanDNA-b5215/dqc_result.json
[2023-03-15 21:02:37,518] [INFO] DFAST_QC completed!
[2023-03-15 21:02:37,518] [INFO] Total running time: 0h0m53s