[2023-03-15 21:48:07,267] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,267] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,267] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd3d5b95-d9c4-470e-839a-f85f8d2d301e/dqc_reference
[2023-03-15 21:48:08,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,884] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,884] [INFO] Running command: cat /var/lib/cwl/stg2dae6de4-0bdd-4f4d-8071-28d0e922d8a6/OceanDNA-b20642.fa | prodigal -d OceanDNA-b20642/cds.fna -a OceanDNA-b20642/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:17,577] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:17,577] [INFO] Task started: HMMsearch
[2023-03-15 21:48:17,577] [INFO] Running command: hmmsearch --tblout OceanDNA-b20642/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd3d5b95-d9c4-470e-839a-f85f8d2d301e/dqc_reference/reference_markers.hmm OceanDNA-b20642/protein.faa > /dev/null
[2023-03-15 21:48:17,742] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:17,742] [INFO] Found 6/6 markers.
[2023-03-15 21:48:17,755] [INFO] Query marker FASTA was written to OceanDNA-b20642/markers.fasta
[2023-03-15 21:48:17,755] [INFO] Task started: Blastn
[2023-03-15 21:48:17,755] [INFO] Running command: blastn -query OceanDNA-b20642/markers.fasta -db /var/lib/cwl/stgcd3d5b95-d9c4-470e-839a-f85f8d2d301e/dqc_reference/reference_markers.fasta -out OceanDNA-b20642/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:18,273] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:18,274] [INFO] Selected 25 target genomes.
[2023-03-15 21:48:18,274] [INFO] Target genome list was writen to OceanDNA-b20642/target_genomes.txt
[2023-03-15 21:48:18,289] [INFO] Task started: fastANI
[2023-03-15 21:48:18,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dae6de4-0bdd-4f4d-8071-28d0e922d8a6/OceanDNA-b20642.fa --refList OceanDNA-b20642/target_genomes.txt --output OceanDNA-b20642/fastani_result.tsv --threads 1
[2023-03-15 21:48:32,496] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:32,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd3d5b95-d9c4-470e-839a-f85f8d2d301e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:32,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd3d5b95-d9c4-470e-839a-f85f8d2d301e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:32,497] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:32,497] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:48:32,497] [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 21:48:32,497] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20642/tc_result.tsv
[2023-03-15 21:48:32,497] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:32,497] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:32,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd3d5b95-d9c4-470e-839a-f85f8d2d301e/dqc_reference/checkm_data
[2023-03-15 21:48:32,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:32,506] [INFO] Task started: CheckM
[2023-03-15 21:48:32,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20642/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20642/checkm_input OceanDNA-b20642/checkm_result
[2023-03-15 21:48:58,987] [INFO] Task succeeded: CheckM
[2023-03-15 21:48:58,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:48:58,989] [INFO] ===== Completeness check finished =====
[2023-03-15 21:48:58,989] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:48:58,989] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20642/markers.fasta)
[2023-03-15 21:48:58,991] [INFO] Task started: Blastn
[2023-03-15 21:48:58,991] [INFO] Running command: blastn -query OceanDNA-b20642/markers.fasta -db /var/lib/cwl/stgcd3d5b95-d9c4-470e-839a-f85f8d2d301e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20642/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:59,702] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:59,702] [INFO] Selected 25 target genomes.
[2023-03-15 21:48:59,703] [INFO] Target genome list was writen to OceanDNA-b20642/target_genomes_gtdb.txt
[2023-03-15 21:48:59,862] [INFO] Task started: fastANI
[2023-03-15 21:48:59,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dae6de4-0bdd-4f4d-8071-28d0e922d8a6/OceanDNA-b20642.fa --refList OceanDNA-b20642/target_genomes_gtdb.txt --output OceanDNA-b20642/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:49:11,278] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:11,280] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:49:11,280] [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_018671635.1	s__JABHHG01 sp018671635	99.105	433	531	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__D37C17;g__JABHHG01	95.0	99.09	99.01	0.82	0.76	4	conclusive
--------------------------------------------------------------------------------
[2023-03-15 21:49:11,281] [INFO] GTDB search result was written to OceanDNA-b20642/result_gtdb.tsv
[2023-03-15 21:49:11,281] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:49:11,281] [INFO] DFAST_QC result json was written to OceanDNA-b20642/dqc_result.json
[2023-03-15 21:49:11,281] [INFO] DFAST_QC completed!
[2023-03-15 21:49:11,281] [INFO] Total running time: 0h1m4s