[2023-03-19 04:29:38,146] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg82a3aec0-63a6-4d27-b270-4543c9a16c42/dqc_reference
[2023-03-19 04:29:39,835] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,835] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,836] [INFO] Running command: cat /var/lib/cwl/stgb47a2f2f-a77b-49c4-b359-a790389751bd/OceanDNA-b17031.fa | prodigal -d OceanDNA-b17031/cds.fna -a OceanDNA-b17031/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:44,747] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:44,747] [INFO] Task started: HMMsearch
[2023-03-19 04:29:44,747] [INFO] Running command: hmmsearch --tblout OceanDNA-b17031/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82a3aec0-63a6-4d27-b270-4543c9a16c42/dqc_reference/reference_markers.hmm OceanDNA-b17031/protein.faa > /dev/null
[2023-03-19 04:29:44,900] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:44,900] [INFO] Found 6/6 markers.
[2023-03-19 04:29:44,911] [INFO] Query marker FASTA was written to OceanDNA-b17031/markers.fasta
[2023-03-19 04:29:44,911] [INFO] Task started: Blastn
[2023-03-19 04:29:44,912] [INFO] Running command: blastn -query OceanDNA-b17031/markers.fasta -db /var/lib/cwl/stg82a3aec0-63a6-4d27-b270-4543c9a16c42/dqc_reference/reference_markers.fasta -out OceanDNA-b17031/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:46,147] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:46,148] [INFO] Selected 17 target genomes.
[2023-03-19 04:29:46,148] [INFO] Target genome list was writen to OceanDNA-b17031/target_genomes.txt
[2023-03-19 04:29:46,159] [INFO] Task started: fastANI
[2023-03-19 04:29:46,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgb47a2f2f-a77b-49c4-b359-a790389751bd/OceanDNA-b17031.fa --refList OceanDNA-b17031/target_genomes.txt --output OceanDNA-b17031/fastani_result.tsv --threads 1
[2023-03-19 04:30:00,874] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:00,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82a3aec0-63a6-4d27-b270-4543c9a16c42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:00,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82a3aec0-63a6-4d27-b270-4543c9a16c42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:00,875] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:00,875] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:30:00,875] [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
--------------------------------------------------------------------------------
[2023-03-19 04:30:00,875] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17031/tc_result.tsv
[2023-03-19 04:30:00,875] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:00,875] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:00,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82a3aec0-63a6-4d27-b270-4543c9a16c42/dqc_reference/checkm_data
[2023-03-19 04:30:00,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:00,882] [INFO] Task started: CheckM
[2023-03-19 04:30:00,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17031/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17031/checkm_input OceanDNA-b17031/checkm_result
[2023-03-19 04:30:19,197] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:19,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:19,199] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:19,200] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:19,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17031/markers.fasta)
[2023-03-19 04:30:19,200] [INFO] Task started: Blastn
[2023-03-19 04:30:19,200] [INFO] Running command: blastn -query OceanDNA-b17031/markers.fasta -db /var/lib/cwl/stg82a3aec0-63a6-4d27-b270-4543c9a16c42/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17031/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:19,983] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:19,984] [INFO] Selected 17 target genomes.
[2023-03-19 04:30:19,984] [INFO] Target genome list was writen to OceanDNA-b17031/target_genomes_gtdb.txt
[2023-03-19 04:30:20,081] [INFO] Task started: fastANI
[2023-03-19 04:30:20,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgb47a2f2f-a77b-49c4-b359-a790389751bd/OceanDNA-b17031.fa --refList OceanDNA-b17031/target_genomes_gtdb.txt --output OceanDNA-b17031/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:28,604] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:28,606] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:28,606] [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_902826595.1	s__2-12-FULL-53-21 sp902826595	77.0089	59	219	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA2774;f__UBA2774;g__2-12-FULL-53-21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001775255.1	s__2-12-FULL-53-21 sp001775255	76.7891	55	219	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA2774;f__UBA2774;g__2-12-FULL-53-21	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:28,607] [INFO] GTDB search result was written to OceanDNA-b17031/result_gtdb.tsv
[2023-03-19 04:30:28,607] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:28,607] [INFO] DFAST_QC result json was written to OceanDNA-b17031/dqc_result.json
[2023-03-19 04:30:28,607] [INFO] DFAST_QC completed!
[2023-03-19 04:30:28,607] [INFO] Total running time: 0h0m50s