[2023-03-18 06:30:24,767] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,771] [INFO] DQC Reference Directory: /var/lib/cwl/stga35e4106-bdcd-4fb6-b3b8-316c45b1c22f/dqc_reference
[2023-03-18 06:30:25,909] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,910] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,910] [INFO] Running command: cat /var/lib/cwl/stg39df90a8-bedb-4036-9081-027bfefd6c1e/OceanDNA-b14778.fa | prodigal -d OceanDNA-b14778/cds.fna -a OceanDNA-b14778/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:31,264] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:31,264] [INFO] Task started: HMMsearch
[2023-03-18 06:30:31,264] [INFO] Running command: hmmsearch --tblout OceanDNA-b14778/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga35e4106-bdcd-4fb6-b3b8-316c45b1c22f/dqc_reference/reference_markers.hmm OceanDNA-b14778/protein.faa > /dev/null
[2023-03-18 06:30:31,396] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:31,397] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg39df90a8-bedb-4036-9081-027bfefd6c1e/OceanDNA-b14778.fa]
[2023-03-18 06:30:31,408] [INFO] Query marker FASTA was written to OceanDNA-b14778/markers.fasta
[2023-03-18 06:30:31,408] [INFO] Task started: Blastn
[2023-03-18 06:30:31,408] [INFO] Running command: blastn -query OceanDNA-b14778/markers.fasta -db /var/lib/cwl/stga35e4106-bdcd-4fb6-b3b8-316c45b1c22f/dqc_reference/reference_markers.fasta -out OceanDNA-b14778/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:31,892] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:31,894] [INFO] Selected 13 target genomes.
[2023-03-18 06:30:31,895] [INFO] Target genome list was writen to OceanDNA-b14778/target_genomes.txt
[2023-03-18 06:30:31,939] [INFO] Task started: fastANI
[2023-03-18 06:30:31,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg39df90a8-bedb-4036-9081-027bfefd6c1e/OceanDNA-b14778.fa --refList OceanDNA-b14778/target_genomes.txt --output OceanDNA-b14778/fastani_result.tsv --threads 1
[2023-03-18 06:30:38,640] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:38,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga35e4106-bdcd-4fb6-b3b8-316c45b1c22f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:38,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga35e4106-bdcd-4fb6-b3b8-316c45b1c22f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:38,641] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:38,641] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:30:38,641] [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 06:30:38,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14778/tc_result.tsv
[2023-03-18 06:30:38,646] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:38,646] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:38,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga35e4106-bdcd-4fb6-b3b8-316c45b1c22f/dqc_reference/checkm_data
[2023-03-18 06:30:38,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:38,670] [INFO] Task started: CheckM
[2023-03-18 06:30:38,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14778/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14778/checkm_input OceanDNA-b14778/checkm_result
[2023-03-18 06:30:57,638] [INFO] Task succeeded: CheckM
[2023-03-18 06:30:57,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:30:57,665] [INFO] ===== Completeness check finished =====
[2023-03-18 06:30:57,665] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:30:57,665] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14778/markers.fasta)
[2023-03-18 06:30:57,667] [INFO] Task started: Blastn
[2023-03-18 06:30:57,667] [INFO] Running command: blastn -query OceanDNA-b14778/markers.fasta -db /var/lib/cwl/stga35e4106-bdcd-4fb6-b3b8-316c45b1c22f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14778/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:58,286] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:58,289] [INFO] Selected 8 target genomes.
[2023-03-18 06:30:58,290] [INFO] Target genome list was writen to OceanDNA-b14778/target_genomes_gtdb.txt
[2023-03-18 06:30:58,489] [INFO] Task started: fastANI
[2023-03-18 06:30:58,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg39df90a8-bedb-4036-9081-027bfefd6c1e/OceanDNA-b14778.fa --refList OceanDNA-b14778/target_genomes_gtdb.txt --output OceanDNA-b14778/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:00,125] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:00,128] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:31:00,128] [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_002721675.1	s__GCA-002700125 sp002721675	99.6197	282	351	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009392285.1	s__GCA-002700125 sp009392285	90.3414	195	351	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239735.1	s__GCA-002700125 sp014239735	82.3802	292	351	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723375.1	s__GCA-002700125 sp002723375	81.5683	204	351	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	96.02	96.02	0.65	0.65	2	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:00,130] [INFO] GTDB search result was written to OceanDNA-b14778/result_gtdb.tsv
[2023-03-18 06:31:00,132] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:00,134] [INFO] DFAST_QC result json was written to OceanDNA-b14778/dqc_result.json
[2023-03-18 06:31:00,134] [INFO] DFAST_QC completed!
[2023-03-18 06:31:00,134] [INFO] Total running time: 0h0m35s