[2023-03-16 00:27:26,858] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:27:26,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:27:26,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg93add0d1-93a9-4e7b-998a-748acae2b7a4/dqc_reference
[2023-03-16 00:27:27,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:27:27,949] [INFO] Task started: Prodigal
[2023-03-16 00:27:27,949] [INFO] Running command: cat /var/lib/cwl/stgf086af72-48bf-4417-8717-54c9a5f07dbd/OceanDNA-b12046.fa | prodigal -d OceanDNA-b12046/cds.fna -a OceanDNA-b12046/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:27:33,652] [INFO] Task succeeded: Prodigal
[2023-03-16 00:27:33,653] [INFO] Task started: HMMsearch
[2023-03-16 00:27:33,653] [INFO] Running command: hmmsearch --tblout OceanDNA-b12046/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93add0d1-93a9-4e7b-998a-748acae2b7a4/dqc_reference/reference_markers.hmm OceanDNA-b12046/protein.faa > /dev/null
[2023-03-16 00:27:33,787] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:27:33,788] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf086af72-48bf-4417-8717-54c9a5f07dbd/OceanDNA-b12046.fa]
[2023-03-16 00:27:33,800] [INFO] Query marker FASTA was written to OceanDNA-b12046/markers.fasta
[2023-03-16 00:27:33,802] [INFO] Task started: Blastn
[2023-03-16 00:27:33,802] [INFO] Running command: blastn -query OceanDNA-b12046/markers.fasta -db /var/lib/cwl/stg93add0d1-93a9-4e7b-998a-748acae2b7a4/dqc_reference/reference_markers.fasta -out OceanDNA-b12046/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:27:34,323] [INFO] Task succeeded: Blastn
[2023-03-16 00:27:34,324] [INFO] Selected 14 target genomes.
[2023-03-16 00:27:34,324] [INFO] Target genome list was writen to OceanDNA-b12046/target_genomes.txt
[2023-03-16 00:27:34,334] [INFO] Task started: fastANI
[2023-03-16 00:27:34,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgf086af72-48bf-4417-8717-54c9a5f07dbd/OceanDNA-b12046.fa --refList OceanDNA-b12046/target_genomes.txt --output OceanDNA-b12046/fastani_result.tsv --threads 1
[2023-03-16 00:27:41,721] [INFO] Task succeeded: fastANI
[2023-03-16 00:27:41,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93add0d1-93a9-4e7b-998a-748acae2b7a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:27:41,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93add0d1-93a9-4e7b-998a-748acae2b7a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:27:41,722] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:27:41,722] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:27:41,722] [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
--------------------------------------------------------------------------------
[2023-03-16 00:27:41,722] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12046/tc_result.tsv
[2023-03-16 00:27:41,722] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:27:41,723] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:27:41,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93add0d1-93a9-4e7b-998a-748acae2b7a4/dqc_reference/checkm_data
[2023-03-16 00:27:41,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:27:41,825] [INFO] Task started: CheckM
[2023-03-16 00:27:41,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12046/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12046/checkm_input OceanDNA-b12046/checkm_result
[2023-03-16 00:28:04,717] [INFO] Task succeeded: CheckM
[2023-03-16 00:28:04,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.30%
Contamintation: 1.14%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-16 00:28:04,719] [INFO] ===== Completeness check finished =====
[2023-03-16 00:28:04,719] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:28:04,719] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12046/markers.fasta)
[2023-03-16 00:28:04,720] [INFO] Task started: Blastn
[2023-03-16 00:28:04,720] [INFO] Running command: blastn -query OceanDNA-b12046/markers.fasta -db /var/lib/cwl/stg93add0d1-93a9-4e7b-998a-748acae2b7a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12046/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:28:05,345] [INFO] Task succeeded: Blastn
[2023-03-16 00:28:05,346] [INFO] Selected 16 target genomes.
[2023-03-16 00:28:05,346] [INFO] Target genome list was writen to OceanDNA-b12046/target_genomes_gtdb.txt
[2023-03-16 00:28:05,594] [INFO] Task started: fastANI
[2023-03-16 00:28:05,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgf086af72-48bf-4417-8717-54c9a5f07dbd/OceanDNA-b12046.fa --refList OceanDNA-b12046/target_genomes_gtdb.txt --output OceanDNA-b12046/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:28:11,699] [INFO] Task succeeded: fastANI
[2023-03-16 00:28:11,702] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:28:11,702] [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_018700255.1	s__UBA974 sp018700255	97.0021	79	101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015660615.1	s__UBA974 sp015660615	92.8523	53	101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339135.1	s__UBA974 sp002339135	79.604	54	101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:28:11,702] [INFO] GTDB search result was written to OceanDNA-b12046/result_gtdb.tsv
[2023-03-16 00:28:11,740] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:28:11,740] [INFO] DFAST_QC result json was written to OceanDNA-b12046/dqc_result.json
[2023-03-16 00:28:11,741] [INFO] DFAST_QC completed!
[2023-03-16 00:28:11,741] [INFO] Total running time: 0h0m45s