[2023-03-18 22:24:43,954] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:24:43,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:24:43,954] [INFO] DQC Reference Directory: /var/lib/cwl/stgba202aab-66f1-4fb2-a611-56dd97eafe42/dqc_reference
[2023-03-18 22:24:45,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:24:45,061] [INFO] Task started: Prodigal
[2023-03-18 22:24:45,062] [INFO] Running command: cat /var/lib/cwl/stg283a2721-8544-43a7-a1b6-81f51706e22c/OceanDNA-b13522.fa | prodigal -d OceanDNA-b13522/cds.fna -a OceanDNA-b13522/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:24:54,281] [INFO] Task succeeded: Prodigal
[2023-03-18 22:24:54,282] [INFO] Task started: HMMsearch
[2023-03-18 22:24:54,282] [INFO] Running command: hmmsearch --tblout OceanDNA-b13522/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba202aab-66f1-4fb2-a611-56dd97eafe42/dqc_reference/reference_markers.hmm OceanDNA-b13522/protein.faa > /dev/null
[2023-03-18 22:24:54,465] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:24:54,466] [INFO] Found 6/6 markers.
[2023-03-18 22:24:54,479] [INFO] Query marker FASTA was written to OceanDNA-b13522/markers.fasta
[2023-03-18 22:24:54,480] [INFO] Task started: Blastn
[2023-03-18 22:24:54,480] [INFO] Running command: blastn -query OceanDNA-b13522/markers.fasta -db /var/lib/cwl/stgba202aab-66f1-4fb2-a611-56dd97eafe42/dqc_reference/reference_markers.fasta -out OceanDNA-b13522/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:24:54,982] [INFO] Task succeeded: Blastn
[2023-03-18 22:24:54,983] [INFO] Selected 13 target genomes.
[2023-03-18 22:24:54,983] [INFO] Target genome list was writen to OceanDNA-b13522/target_genomes.txt
[2023-03-18 22:24:54,990] [INFO] Task started: fastANI
[2023-03-18 22:24:54,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg283a2721-8544-43a7-a1b6-81f51706e22c/OceanDNA-b13522.fa --refList OceanDNA-b13522/target_genomes.txt --output OceanDNA-b13522/fastani_result.tsv --threads 1
[2023-03-18 22:25:01,167] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:01,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba202aab-66f1-4fb2-a611-56dd97eafe42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:25:01,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba202aab-66f1-4fb2-a611-56dd97eafe42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:25:01,168] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:25:01,168] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:25:01,168] [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 22:25:01,168] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13522/tc_result.tsv
[2023-03-18 22:25:01,168] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:25:01,168] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:25:01,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba202aab-66f1-4fb2-a611-56dd97eafe42/dqc_reference/checkm_data
[2023-03-18 22:25:01,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:25:01,175] [INFO] Task started: CheckM
[2023-03-18 22:25:01,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13522/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13522/checkm_input OceanDNA-b13522/checkm_result
[2023-03-18 22:25:28,321] [INFO] Task succeeded: CheckM
[2023-03-18 22:25:28,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:25:28,323] [INFO] ===== Completeness check finished =====
[2023-03-18 22:25:28,323] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:25:28,324] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13522/markers.fasta)
[2023-03-18 22:25:28,325] [INFO] Task started: Blastn
[2023-03-18 22:25:28,325] [INFO] Running command: blastn -query OceanDNA-b13522/markers.fasta -db /var/lib/cwl/stgba202aab-66f1-4fb2-a611-56dd97eafe42/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13522/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:28,994] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:28,995] [INFO] Selected 20 target genomes.
[2023-03-18 22:25:28,995] [INFO] Target genome list was writen to OceanDNA-b13522/target_genomes_gtdb.txt
[2023-03-18 22:25:29,033] [INFO] Task started: fastANI
[2023-03-18 22:25:29,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg283a2721-8544-43a7-a1b6-81f51706e22c/OceanDNA-b13522.fa --refList OceanDNA-b13522/target_genomes_gtdb.txt --output OceanDNA-b13522/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:25:36,341] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:36,344] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:25:36,344] [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_002296125.1	s__UBA11657 sp002296125	99.5354	481	564	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.33	99.25	0.80	0.79	3	conclusive
GCA_002377585.1	s__UBA11657 sp002377585	77.6896	85	564	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.07	98.64	0.89	0.85	4	-
GCA_002311455.1	s__UBA11657 sp002311455	76.6792	53	564	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:25:36,344] [INFO] GTDB search result was written to OceanDNA-b13522/result_gtdb.tsv
[2023-03-18 22:25:36,345] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:25:36,345] [INFO] DFAST_QC result json was written to OceanDNA-b13522/dqc_result.json
[2023-03-18 22:25:36,345] [INFO] DFAST_QC completed!
[2023-03-18 22:25:36,346] [INFO] Total running time: 0h0m52s