[2023-03-16 05:52:41,062] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,062] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,062] [INFO] DQC Reference Directory: /var/lib/cwl/stgb93d21c1-3b66-4a9a-8894-a3f219c4a208/dqc_reference
[2023-03-16 05:52:42,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,139] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,139] [INFO] Running command: cat /var/lib/cwl/stg4de9ae81-6219-4ead-88f2-d1bf3782aaae/OceanDNA-b16220.fa | prodigal -d OceanDNA-b16220/cds.fna -a OceanDNA-b16220/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:53:05,225] [INFO] Task succeeded: Prodigal
[2023-03-16 05:53:05,226] [INFO] Task started: HMMsearch
[2023-03-16 05:53:05,226] [INFO] Running command: hmmsearch --tblout OceanDNA-b16220/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb93d21c1-3b66-4a9a-8894-a3f219c4a208/dqc_reference/reference_markers.hmm OceanDNA-b16220/protein.faa > /dev/null
[2023-03-16 05:53:05,461] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:53:05,462] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4de9ae81-6219-4ead-88f2-d1bf3782aaae/OceanDNA-b16220.fa]
[2023-03-16 05:53:05,489] [INFO] Query marker FASTA was written to OceanDNA-b16220/markers.fasta
[2023-03-16 05:53:05,490] [INFO] Task started: Blastn
[2023-03-16 05:53:05,490] [INFO] Running command: blastn -query OceanDNA-b16220/markers.fasta -db /var/lib/cwl/stgb93d21c1-3b66-4a9a-8894-a3f219c4a208/dqc_reference/reference_markers.fasta -out OceanDNA-b16220/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:06,015] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:06,086] [INFO] Selected 15 target genomes.
[2023-03-16 05:53:06,086] [INFO] Target genome list was writen to OceanDNA-b16220/target_genomes.txt
[2023-03-16 05:53:06,097] [INFO] Task started: fastANI
[2023-03-16 05:53:06,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg4de9ae81-6219-4ead-88f2-d1bf3782aaae/OceanDNA-b16220.fa --refList OceanDNA-b16220/target_genomes.txt --output OceanDNA-b16220/fastani_result.tsv --threads 1
[2023-03-16 05:53:17,586] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:17,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb93d21c1-3b66-4a9a-8894-a3f219c4a208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:53:17,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb93d21c1-3b66-4a9a-8894-a3f219c4a208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:53:17,587] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:53:17,587] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:53:17,587] [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
--------------------------------------------------------------------------------
[2023-03-16 05:53:17,587] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16220/tc_result.tsv
[2023-03-16 05:53:17,588] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:53:17,588] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:53:17,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb93d21c1-3b66-4a9a-8894-a3f219c4a208/dqc_reference/checkm_data
[2023-03-16 05:53:17,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:53:17,607] [INFO] Task started: CheckM
[2023-03-16 05:53:17,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16220/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16220/checkm_input OceanDNA-b16220/checkm_result
[2023-03-16 05:54:13,041] [INFO] Task succeeded: CheckM
[2023-03-16 05:54:13,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:54:13,049] [INFO] ===== Completeness check finished =====
[2023-03-16 05:54:13,049] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:54:13,050] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16220/markers.fasta)
[2023-03-16 05:54:13,051] [INFO] Task started: Blastn
[2023-03-16 05:54:13,051] [INFO] Running command: blastn -query OceanDNA-b16220/markers.fasta -db /var/lib/cwl/stgb93d21c1-3b66-4a9a-8894-a3f219c4a208/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16220/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:54:13,721] [INFO] Task succeeded: Blastn
[2023-03-16 05:54:13,725] [INFO] Selected 19 target genomes.
[2023-03-16 05:54:13,725] [INFO] Target genome list was writen to OceanDNA-b16220/target_genomes_gtdb.txt
[2023-03-16 05:54:13,749] [INFO] Task started: fastANI
[2023-03-16 05:54:13,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg4de9ae81-6219-4ead-88f2-d1bf3782aaae/OceanDNA-b16220.fa --refList OceanDNA-b16220/target_genomes_gtdb.txt --output OceanDNA-b16220/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:54:29,124] [INFO] Task succeeded: fastANI
[2023-03-16 05:54:29,129] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:54:29,129] [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_001314865.1	s__Phormidesmis priestleyi_B	76.7069	265	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242035.1	s__Phormidesmis foveolarum	76.6294	221	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286735.1	s__Phormidesmis sp002286735	76.5157	231	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242115.1	s__Phormidesmis priestleyi_A	76.3724	215	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207105.1	s__Phormidesmis sp015207105	76.3631	192	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033015.1	s__Phormidesmis sp012033015	76.2876	214	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155595.1	s__Phormidesmis sp000155595	76.0506	133	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695395.1	s__Nodosilinea sp014695395	75.0308	50	1335	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:54:29,130] [INFO] GTDB search result was written to OceanDNA-b16220/result_gtdb.tsv
[2023-03-16 05:54:29,131] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:54:29,132] [INFO] DFAST_QC result json was written to OceanDNA-b16220/dqc_result.json
[2023-03-16 05:54:29,132] [INFO] DFAST_QC completed!
[2023-03-16 05:54:29,132] [INFO] Total running time: 0h1m48s