[2023-03-14 12:25:41,450] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,450] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg28dcb327-6a10-4273-b6b9-0027e861ff93/dqc_reference
[2023-03-14 12:25:42,577] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,578] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,578] [INFO] Running command: cat /var/lib/cwl/stg477caafe-8d01-41b9-b44f-d24b6189d062/OceanDNA-b21936.fa | prodigal -d OceanDNA-b21936/cds.fna -a OceanDNA-b21936/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:47,292] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:47,293] [INFO] Task started: HMMsearch
[2023-03-14 12:25:47,293] [INFO] Running command: hmmsearch --tblout OceanDNA-b21936/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28dcb327-6a10-4273-b6b9-0027e861ff93/dqc_reference/reference_markers.hmm OceanDNA-b21936/protein.faa > /dev/null
[2023-03-14 12:25:47,466] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:47,466] [INFO] Found 6/6 markers.
[2023-03-14 12:25:47,472] [INFO] Query marker FASTA was written to OceanDNA-b21936/markers.fasta
[2023-03-14 12:25:47,472] [INFO] Task started: Blastn
[2023-03-14 12:25:47,472] [INFO] Running command: blastn -query OceanDNA-b21936/markers.fasta -db /var/lib/cwl/stg28dcb327-6a10-4273-b6b9-0027e861ff93/dqc_reference/reference_markers.fasta -out OceanDNA-b21936/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:47,974] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:47,974] [INFO] Selected 13 target genomes.
[2023-03-14 12:25:47,975] [INFO] Target genome list was writen to OceanDNA-b21936/target_genomes.txt
[2023-03-14 12:25:47,984] [INFO] Task started: fastANI
[2023-03-14 12:25:47,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg477caafe-8d01-41b9-b44f-d24b6189d062/OceanDNA-b21936.fa --refList OceanDNA-b21936/target_genomes.txt --output OceanDNA-b21936/fastani_result.tsv --threads 1
[2023-03-14 12:25:55,273] [INFO] Task succeeded: fastANI
[2023-03-14 12:25:55,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28dcb327-6a10-4273-b6b9-0027e861ff93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:25:55,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28dcb327-6a10-4273-b6b9-0027e861ff93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:25:55,274] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:25:55,274] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:25:55,274] [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
--------------------------------------------------------------------------------
[2023-03-14 12:25:55,274] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21936/tc_result.tsv
[2023-03-14 12:25:55,274] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:25:55,274] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:25:55,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28dcb327-6a10-4273-b6b9-0027e861ff93/dqc_reference/checkm_data
[2023-03-14 12:25:55,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:25:55,278] [INFO] Task started: CheckM
[2023-03-14 12:25:55,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21936/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21936/checkm_input OceanDNA-b21936/checkm_result
[2023-03-14 12:26:14,523] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:14,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.76%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:14,525] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:14,525] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:14,525] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21936/markers.fasta)
[2023-03-14 12:26:14,526] [INFO] Task started: Blastn
[2023-03-14 12:26:14,526] [INFO] Running command: blastn -query OceanDNA-b21936/markers.fasta -db /var/lib/cwl/stg28dcb327-6a10-4273-b6b9-0027e861ff93/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21936/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:15,220] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:15,221] [INFO] Selected 19 target genomes.
[2023-03-14 12:26:15,221] [INFO] Target genome list was writen to OceanDNA-b21936/target_genomes_gtdb.txt
[2023-03-14 12:26:15,246] [INFO] Task started: fastANI
[2023-03-14 12:26:15,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg477caafe-8d01-41b9-b44f-d24b6189d062/OceanDNA-b21936.fa --refList OceanDNA-b21936/target_genomes_gtdb.txt --output OceanDNA-b21936/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:26:19,201] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:19,203] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:26:19,203] [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_002422025.1	s__UBA918 sp002422025	80.7796	124	205	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA918;g__UBA918	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:26:19,203] [INFO] GTDB search result was written to OceanDNA-b21936/result_gtdb.tsv
[2023-03-14 12:26:19,204] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:26:19,204] [INFO] DFAST_QC result json was written to OceanDNA-b21936/dqc_result.json
[2023-03-14 12:26:19,204] [INFO] DFAST_QC completed!
[2023-03-14 12:26:19,204] [INFO] Total running time: 0h0m38s