[2023-03-18 06:02:58,280] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:02:58,281] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:02:58,281] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd2e4992-fed1-406c-a225-cfcc701eed7c/dqc_reference
[2023-03-18 06:03:00,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:03:00,171] [INFO] Task started: Prodigal
[2023-03-18 06:03:00,171] [INFO] Running command: cat /var/lib/cwl/stg918dc6df-8b0c-489c-ac44-0455bb996504/OceanDNA-b10919.fa | prodigal -d OceanDNA-b10919/cds.fna -a OceanDNA-b10919/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:03:06,913] [INFO] Task succeeded: Prodigal
[2023-03-18 06:03:06,913] [INFO] Task started: HMMsearch
[2023-03-18 06:03:06,913] [INFO] Running command: hmmsearch --tblout OceanDNA-b10919/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd2e4992-fed1-406c-a225-cfcc701eed7c/dqc_reference/reference_markers.hmm OceanDNA-b10919/protein.faa > /dev/null
[2023-03-18 06:03:07,057] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:03:07,058] [INFO] Found 6/6 markers.
[2023-03-18 06:03:07,069] [INFO] Query marker FASTA was written to OceanDNA-b10919/markers.fasta
[2023-03-18 06:03:07,070] [INFO] Task started: Blastn
[2023-03-18 06:03:07,070] [INFO] Running command: blastn -query OceanDNA-b10919/markers.fasta -db /var/lib/cwl/stgdd2e4992-fed1-406c-a225-cfcc701eed7c/dqc_reference/reference_markers.fasta -out OceanDNA-b10919/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:03:07,623] [INFO] Task succeeded: Blastn
[2023-03-18 06:03:07,624] [INFO] Selected 29 target genomes.
[2023-03-18 06:03:07,624] [INFO] Target genome list was writen to OceanDNA-b10919/target_genomes.txt
[2023-03-18 06:03:07,902] [INFO] Task started: fastANI
[2023-03-18 06:03:07,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg918dc6df-8b0c-489c-ac44-0455bb996504/OceanDNA-b10919.fa --refList OceanDNA-b10919/target_genomes.txt --output OceanDNA-b10919/fastani_result.tsv --threads 1
[2023-03-18 06:03:22,559] [INFO] Task succeeded: fastANI
[2023-03-18 06:03:22,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd2e4992-fed1-406c-a225-cfcc701eed7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:03:22,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd2e4992-fed1-406c-a225-cfcc701eed7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:03:22,560] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:03:22,560] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:03:22,560] [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 06:03:22,560] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10919/tc_result.tsv
[2023-03-18 06:03:22,560] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:03:22,560] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:03:22,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd2e4992-fed1-406c-a225-cfcc701eed7c/dqc_reference/checkm_data
[2023-03-18 06:03:22,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:03:22,567] [INFO] Task started: CheckM
[2023-03-18 06:03:22,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10919/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10919/checkm_input OceanDNA-b10919/checkm_result
[2023-03-18 06:03:45,127] [INFO] Task succeeded: CheckM
[2023-03-18 06:03:45,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.06%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:03:45,129] [INFO] ===== Completeness check finished =====
[2023-03-18 06:03:45,130] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:03:45,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10919/markers.fasta)
[2023-03-18 06:03:45,131] [INFO] Task started: Blastn
[2023-03-18 06:03:45,131] [INFO] Running command: blastn -query OceanDNA-b10919/markers.fasta -db /var/lib/cwl/stgdd2e4992-fed1-406c-a225-cfcc701eed7c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10919/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:03:46,030] [INFO] Task succeeded: Blastn
[2023-03-18 06:03:46,031] [INFO] Selected 22 target genomes.
[2023-03-18 06:03:46,031] [INFO] Target genome list was writen to OceanDNA-b10919/target_genomes_gtdb.txt
[2023-03-18 06:03:46,653] [INFO] Task started: fastANI
[2023-03-18 06:03:46,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg918dc6df-8b0c-489c-ac44-0455bb996504/OceanDNA-b10919.fa --refList OceanDNA-b10919/target_genomes_gtdb.txt --output OceanDNA-b10919/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:03:54,732] [INFO] Task succeeded: fastANI
[2023-03-18 06:03:54,736] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:03:54,736] [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_011526285.1	s__UBA7428 sp011526285	78.2747	67	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526275.1	s__UBA7428 sp011526275	77.9592	75	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478905.1	s__UBA7428 sp905478905	77.8916	75	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-18 06:03:54,736] [INFO] GTDB search result was written to OceanDNA-b10919/result_gtdb.tsv
[2023-03-18 06:03:54,736] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:03:54,737] [INFO] DFAST_QC result json was written to OceanDNA-b10919/dqc_result.json
[2023-03-18 06:03:54,737] [INFO] DFAST_QC completed!
[2023-03-18 06:03:54,737] [INFO] Total running time: 0h0m56s