[2023-03-15 23:56:02,655] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:56:02,656] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:56:02,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg69b3b131-2bb9-442f-950b-513e8b204f73/dqc_reference
[2023-03-15 23:56:03,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:56:03,781] [INFO] Task started: Prodigal
[2023-03-15 23:56:03,782] [INFO] Running command: cat /var/lib/cwl/stgeef2cd18-1b77-4598-80ef-f0e0aeee01d6/OceanDNA-b1347.fa | prodigal -d OceanDNA-b1347/cds.fna -a OceanDNA-b1347/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:56:20,427] [INFO] Task succeeded: Prodigal
[2023-03-15 23:56:20,428] [INFO] Task started: HMMsearch
[2023-03-15 23:56:20,428] [INFO] Running command: hmmsearch --tblout OceanDNA-b1347/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69b3b131-2bb9-442f-950b-513e8b204f73/dqc_reference/reference_markers.hmm OceanDNA-b1347/protein.faa > /dev/null
[2023-03-15 23:56:20,626] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:56:20,627] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeef2cd18-1b77-4598-80ef-f0e0aeee01d6/OceanDNA-b1347.fa]
[2023-03-15 23:56:20,649] [INFO] Query marker FASTA was written to OceanDNA-b1347/markers.fasta
[2023-03-15 23:56:20,650] [INFO] Task started: Blastn
[2023-03-15 23:56:20,650] [INFO] Running command: blastn -query OceanDNA-b1347/markers.fasta -db /var/lib/cwl/stg69b3b131-2bb9-442f-950b-513e8b204f73/dqc_reference/reference_markers.fasta -out OceanDNA-b1347/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:56:21,187] [INFO] Task succeeded: Blastn
[2023-03-15 23:56:21,190] [INFO] Selected 19 target genomes.
[2023-03-15 23:56:21,190] [INFO] Target genome list was writen to OceanDNA-b1347/target_genomes.txt
[2023-03-15 23:56:21,249] [INFO] Task started: fastANI
[2023-03-15 23:56:21,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef2cd18-1b77-4598-80ef-f0e0aeee01d6/OceanDNA-b1347.fa --refList OceanDNA-b1347/target_genomes.txt --output OceanDNA-b1347/fastani_result.tsv --threads 1
[2023-03-15 23:56:32,786] [INFO] Task succeeded: fastANI
[2023-03-15 23:56:32,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69b3b131-2bb9-442f-950b-513e8b204f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:56:32,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69b3b131-2bb9-442f-950b-513e8b204f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:56:32,786] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:56:32,786] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:56:32,787] [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 23:56:32,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1347/tc_result.tsv
[2023-03-15 23:56:32,788] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:56:32,788] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:56:32,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69b3b131-2bb9-442f-950b-513e8b204f73/dqc_reference/checkm_data
[2023-03-15 23:56:32,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:56:32,800] [INFO] Task started: CheckM
[2023-03-15 23:56:32,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1347/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1347/checkm_input OceanDNA-b1347/checkm_result
[2023-03-15 23:57:17,159] [INFO] Task succeeded: CheckM
[2023-03-15 23:57:17,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:57:17,260] [INFO] ===== Completeness check finished =====
[2023-03-15 23:57:17,260] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:57:17,261] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1347/markers.fasta)
[2023-03-15 23:57:17,262] [INFO] Task started: Blastn
[2023-03-15 23:57:17,262] [INFO] Running command: blastn -query OceanDNA-b1347/markers.fasta -db /var/lib/cwl/stg69b3b131-2bb9-442f-950b-513e8b204f73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1347/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:57:18,027] [INFO] Task succeeded: Blastn
[2023-03-15 23:57:18,031] [INFO] Selected 14 target genomes.
[2023-03-15 23:57:18,031] [INFO] Target genome list was writen to OceanDNA-b1347/target_genomes_gtdb.txt
[2023-03-15 23:57:18,089] [INFO] Task started: fastANI
[2023-03-15 23:57:18,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef2cd18-1b77-4598-80ef-f0e0aeee01d6/OceanDNA-b1347.fa --refList OceanDNA-b1347/target_genomes_gtdb.txt --output OceanDNA-b1347/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:57:25,061] [INFO] Task succeeded: fastANI
[2023-03-15 23:57:25,064] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:57:25,064] [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_001025035.1	s__IMCC26207 sp001025035	94.209	829	873	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__IMCC26207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009700815.1	s__IMCC26207 sp009700815	93.1851	551	873	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__IMCC26207	95.0	98.59	98.33	0.78	0.75	5	-
GCA_009701845.1	s__IMCC26207 sp009701845	80.619	459	873	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__IMCC26207	95.0	99.35	99.30	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-15 23:57:25,065] [INFO] GTDB search result was written to OceanDNA-b1347/result_gtdb.tsv
[2023-03-15 23:57:25,067] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:57:25,070] [INFO] DFAST_QC result json was written to OceanDNA-b1347/dqc_result.json
[2023-03-15 23:57:25,070] [INFO] DFAST_QC completed!
[2023-03-15 23:57:25,070] [INFO] Total running time: 0h1m22s