[2023-03-18 04:38:00,416] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:38:00,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:38:00,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a28e47b-bb52-4445-beee-db7721f4e1f6/dqc_reference
[2023-03-18 04:38:01,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:01,521] [INFO] Task started: Prodigal
[2023-03-18 04:38:01,521] [INFO] Running command: cat /var/lib/cwl/stg631b03ca-eaef-4383-aaa0-36c72f867967/OceanDNA-b3461.fa | prodigal -d OceanDNA-b3461/cds.fna -a OceanDNA-b3461/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:23,701] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:23,702] [INFO] Task started: HMMsearch
[2023-03-18 04:38:23,702] [INFO] Running command: hmmsearch --tblout OceanDNA-b3461/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a28e47b-bb52-4445-beee-db7721f4e1f6/dqc_reference/reference_markers.hmm OceanDNA-b3461/protein.faa > /dev/null
[2023-03-18 04:38:23,927] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:23,928] [INFO] Found 6/6 markers.
[2023-03-18 04:38:23,952] [INFO] Query marker FASTA was written to OceanDNA-b3461/markers.fasta
[2023-03-18 04:38:23,953] [INFO] Task started: Blastn
[2023-03-18 04:38:23,953] [INFO] Running command: blastn -query OceanDNA-b3461/markers.fasta -db /var/lib/cwl/stg6a28e47b-bb52-4445-beee-db7721f4e1f6/dqc_reference/reference_markers.fasta -out OceanDNA-b3461/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:24,484] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:24,485] [INFO] Selected 25 target genomes.
[2023-03-18 04:38:24,486] [INFO] Target genome list was writen to OceanDNA-b3461/target_genomes.txt
[2023-03-18 04:38:24,500] [INFO] Task started: fastANI
[2023-03-18 04:38:24,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg631b03ca-eaef-4383-aaa0-36c72f867967/OceanDNA-b3461.fa --refList OceanDNA-b3461/target_genomes.txt --output OceanDNA-b3461/fastani_result.tsv --threads 1
[2023-03-18 04:38:38,852] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:38,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a28e47b-bb52-4445-beee-db7721f4e1f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:38,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a28e47b-bb52-4445-beee-db7721f4e1f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:38,852] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:38:38,853] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:38:38,853] [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 04:38:38,853] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3461/tc_result.tsv
[2023-03-18 04:38:38,853] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:38,854] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:38,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a28e47b-bb52-4445-beee-db7721f4e1f6/dqc_reference/checkm_data
[2023-03-18 04:38:38,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:38,862] [INFO] Task started: CheckM
[2023-03-18 04:38:38,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3461/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3461/checkm_input OceanDNA-b3461/checkm_result
[2023-03-18 04:39:35,594] [INFO] Task succeeded: CheckM
[2023-03-18 04:39:35,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:39:35,598] [INFO] ===== Completeness check finished =====
[2023-03-18 04:39:35,598] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:39:35,598] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3461/markers.fasta)
[2023-03-18 04:39:35,599] [INFO] Task started: Blastn
[2023-03-18 04:39:35,599] [INFO] Running command: blastn -query OceanDNA-b3461/markers.fasta -db /var/lib/cwl/stg6a28e47b-bb52-4445-beee-db7721f4e1f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3461/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:36,297] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:36,299] [INFO] Selected 30 target genomes.
[2023-03-18 04:39:36,299] [INFO] Target genome list was writen to OceanDNA-b3461/target_genomes_gtdb.txt
[2023-03-18 04:39:36,325] [INFO] Task started: fastANI
[2023-03-18 04:39:36,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg631b03ca-eaef-4383-aaa0-36c72f867967/OceanDNA-b3461.fa --refList OceanDNA-b3461/target_genomes_gtdb.txt --output OceanDNA-b3461/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:39:50,936] [INFO] Task succeeded: fastANI
[2023-03-18 04:39:50,938] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:39:50,938] [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_016124515.1	s__JACPUW01 sp016124515	76.3063	88	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__CAILMK01;f__JACPUW01;g__JACPUW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:39:50,938] [INFO] GTDB search result was written to OceanDNA-b3461/result_gtdb.tsv
[2023-03-18 04:39:50,938] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:39:50,939] [INFO] DFAST_QC result json was written to OceanDNA-b3461/dqc_result.json
[2023-03-18 04:39:50,939] [INFO] DFAST_QC completed!
[2023-03-18 04:39:50,939] [INFO] Total running time: 0h1m51s