[2023-03-16 04:24:46,335] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg6655247b-bf20-4b5c-a5a6-5cf2f452dc7d/dqc_reference
[2023-03-16 04:24:48,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,114] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,114] [INFO] Running command: cat /var/lib/cwl/stg0ea3c34e-57e1-4509-ac7b-ee324d36e6be/OceanDNA-b23003.fa | prodigal -d OceanDNA-b23003/cds.fna -a OceanDNA-b23003/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:23,972] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:23,972] [INFO] Task started: HMMsearch
[2023-03-16 04:25:23,972] [INFO] Running command: hmmsearch --tblout OceanDNA-b23003/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6655247b-bf20-4b5c-a5a6-5cf2f452dc7d/dqc_reference/reference_markers.hmm OceanDNA-b23003/protein.faa > /dev/null
[2023-03-16 04:25:24,222] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:24,222] [INFO] Found 6/6 markers.
[2023-03-16 04:25:24,257] [INFO] Query marker FASTA was written to OceanDNA-b23003/markers.fasta
[2023-03-16 04:25:24,260] [INFO] Task started: Blastn
[2023-03-16 04:25:24,260] [INFO] Running command: blastn -query OceanDNA-b23003/markers.fasta -db /var/lib/cwl/stg6655247b-bf20-4b5c-a5a6-5cf2f452dc7d/dqc_reference/reference_markers.fasta -out OceanDNA-b23003/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:24,925] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:24,926] [INFO] Selected 21 target genomes.
[2023-03-16 04:25:24,926] [INFO] Target genome list was writen to OceanDNA-b23003/target_genomes.txt
[2023-03-16 04:25:24,939] [INFO] Task started: fastANI
[2023-03-16 04:25:24,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea3c34e-57e1-4509-ac7b-ee324d36e6be/OceanDNA-b23003.fa --refList OceanDNA-b23003/target_genomes.txt --output OceanDNA-b23003/fastani_result.tsv --threads 1
[2023-03-16 04:25:39,932] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:39,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6655247b-bf20-4b5c-a5a6-5cf2f452dc7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:39,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6655247b-bf20-4b5c-a5a6-5cf2f452dc7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:39,933] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:39,933] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:25:39,933] [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 04:25:39,933] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23003/tc_result.tsv
[2023-03-16 04:25:39,933] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:39,933] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:39,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6655247b-bf20-4b5c-a5a6-5cf2f452dc7d/dqc_reference/checkm_data
[2023-03-16 04:25:39,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:39,942] [INFO] Task started: CheckM
[2023-03-16 04:25:39,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23003/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23003/checkm_input OceanDNA-b23003/checkm_result
[2023-03-16 04:27:06,237] [INFO] Task succeeded: CheckM
[2023-03-16 04:27:06,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:27:06,241] [INFO] ===== Completeness check finished =====
[2023-03-16 04:27:06,241] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:27:06,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23003/markers.fasta)
[2023-03-16 04:27:06,242] [INFO] Task started: Blastn
[2023-03-16 04:27:06,242] [INFO] Running command: blastn -query OceanDNA-b23003/markers.fasta -db /var/lib/cwl/stg6655247b-bf20-4b5c-a5a6-5cf2f452dc7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23003/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:27:06,956] [INFO] Task succeeded: Blastn
[2023-03-16 04:27:06,957] [INFO] Selected 24 target genomes.
[2023-03-16 04:27:06,958] [INFO] Target genome list was writen to OceanDNA-b23003/target_genomes_gtdb.txt
[2023-03-16 04:27:06,977] [INFO] Task started: fastANI
[2023-03-16 04:27:06,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea3c34e-57e1-4509-ac7b-ee324d36e6be/OceanDNA-b23003.fa --refList OceanDNA-b23003/target_genomes_gtdb.txt --output OceanDNA-b23003/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:27:24,730] [INFO] Task succeeded: fastANI
[2023-03-16 04:27:24,732] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:27:24,733] [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_016709875.1	s__JADJLZ01 sp016709875	75.2509	52	1367	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	75.0273	50	1367	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:27:24,733] [INFO] GTDB search result was written to OceanDNA-b23003/result_gtdb.tsv
[2023-03-16 04:27:24,733] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:27:24,733] [INFO] DFAST_QC result json was written to OceanDNA-b23003/dqc_result.json
[2023-03-16 04:27:24,734] [INFO] DFAST_QC completed!
[2023-03-16 04:27:24,734] [INFO] Total running time: 0h2m38s