[2023-03-18 00:35:04,528] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,528] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg447f7647-0c15-4fda-96a6-959bfc1ca2af/dqc_reference
[2023-03-18 00:35:05,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,636] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,637] [INFO] Running command: cat /var/lib/cwl/stgfe18ac7c-c762-4fa0-a851-38415feac84f/OceanDNA-b19603.fa | prodigal -d OceanDNA-b19603/cds.fna -a OceanDNA-b19603/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:11,350] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:11,351] [INFO] Task started: HMMsearch
[2023-03-18 00:35:11,351] [INFO] Running command: hmmsearch --tblout OceanDNA-b19603/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg447f7647-0c15-4fda-96a6-959bfc1ca2af/dqc_reference/reference_markers.hmm OceanDNA-b19603/protein.faa > /dev/null
[2023-03-18 00:35:11,546] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:11,547] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfe18ac7c-c762-4fa0-a851-38415feac84f/OceanDNA-b19603.fa]
[2023-03-18 00:35:11,561] [INFO] Query marker FASTA was written to OceanDNA-b19603/markers.fasta
[2023-03-18 00:35:11,561] [INFO] Task started: Blastn
[2023-03-18 00:35:11,561] [INFO] Running command: blastn -query OceanDNA-b19603/markers.fasta -db /var/lib/cwl/stg447f7647-0c15-4fda-96a6-959bfc1ca2af/dqc_reference/reference_markers.fasta -out OceanDNA-b19603/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:12,055] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:12,055] [INFO] Selected 10 target genomes.
[2023-03-18 00:35:12,056] [INFO] Target genome list was writen to OceanDNA-b19603/target_genomes.txt
[2023-03-18 00:35:12,061] [INFO] Task started: fastANI
[2023-03-18 00:35:12,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe18ac7c-c762-4fa0-a851-38415feac84f/OceanDNA-b19603.fa --refList OceanDNA-b19603/target_genomes.txt --output OceanDNA-b19603/fastani_result.tsv --threads 1
[2023-03-18 00:35:16,094] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:16,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg447f7647-0c15-4fda-96a6-959bfc1ca2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:16,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg447f7647-0c15-4fda-96a6-959bfc1ca2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:16,095] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:16,095] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:35:16,095] [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 00:35:16,095] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19603/tc_result.tsv
[2023-03-18 00:35:16,095] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:16,096] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:16,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg447f7647-0c15-4fda-96a6-959bfc1ca2af/dqc_reference/checkm_data
[2023-03-18 00:35:16,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:16,101] [INFO] Task started: CheckM
[2023-03-18 00:35:16,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19603/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19603/checkm_input OceanDNA-b19603/checkm_result
[2023-03-18 00:35:37,127] [INFO] Task succeeded: CheckM
[2023-03-18 00:35:37,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:35:37,130] [INFO] ===== Completeness check finished =====
[2023-03-18 00:35:37,130] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:35:37,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19603/markers.fasta)
[2023-03-18 00:35:37,130] [INFO] Task started: Blastn
[2023-03-18 00:35:37,130] [INFO] Running command: blastn -query OceanDNA-b19603/markers.fasta -db /var/lib/cwl/stg447f7647-0c15-4fda-96a6-959bfc1ca2af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19603/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:37,776] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:37,777] [INFO] Selected 23 target genomes.
[2023-03-18 00:35:37,777] [INFO] Target genome list was writen to OceanDNA-b19603/target_genomes_gtdb.txt
[2023-03-18 00:35:37,798] [INFO] Task started: fastANI
[2023-03-18 00:35:37,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe18ac7c-c762-4fa0-a851-38415feac84f/OceanDNA-b19603.fa --refList OceanDNA-b19603/target_genomes_gtdb.txt --output OceanDNA-b19603/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:35:44,817] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:44,818] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:35:44,818] [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
--------------------------------------------------------------------------------
[2023-03-18 00:35:44,818] [INFO] GTDB search result was written to OceanDNA-b19603/result_gtdb.tsv
[2023-03-18 00:35:44,818] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:35:44,818] [INFO] DFAST_QC result json was written to OceanDNA-b19603/dqc_result.json
[2023-03-18 00:35:44,819] [INFO] DFAST_QC completed!
[2023-03-18 00:35:44,819] [INFO] Total running time: 0h0m40s