[2023-03-17 23:54:10,800] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:54:10,801] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:54:10,801] [INFO] DQC Reference Directory: /var/lib/cwl/stgca77d718-0d8c-4c14-87f2-0372d34bb219/dqc_reference
[2023-03-17 23:54:11,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:54:11,982] [INFO] Task started: Prodigal
[2023-03-17 23:54:11,982] [INFO] Running command: cat /var/lib/cwl/stg554813a7-9675-485f-a0d2-cb361a17a6bd/OceanDNA-b41615.fa | prodigal -d OceanDNA-b41615/cds.fna -a OceanDNA-b41615/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:54:21,024] [INFO] Task succeeded: Prodigal
[2023-03-17 23:54:21,024] [INFO] Task started: HMMsearch
[2023-03-17 23:54:21,024] [INFO] Running command: hmmsearch --tblout OceanDNA-b41615/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca77d718-0d8c-4c14-87f2-0372d34bb219/dqc_reference/reference_markers.hmm OceanDNA-b41615/protein.faa > /dev/null
[2023-03-17 23:54:21,190] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:54:21,191] [INFO] Found 6/6 markers.
[2023-03-17 23:54:21,213] [INFO] Query marker FASTA was written to OceanDNA-b41615/markers.fasta
[2023-03-17 23:54:21,213] [INFO] Task started: Blastn
[2023-03-17 23:54:21,213] [INFO] Running command: blastn -query OceanDNA-b41615/markers.fasta -db /var/lib/cwl/stgca77d718-0d8c-4c14-87f2-0372d34bb219/dqc_reference/reference_markers.fasta -out OceanDNA-b41615/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:54:21,792] [INFO] Task succeeded: Blastn
[2023-03-17 23:54:21,799] [INFO] Selected 28 target genomes.
[2023-03-17 23:54:21,799] [INFO] Target genome list was writen to OceanDNA-b41615/target_genomes.txt
[2023-03-17 23:54:21,821] [INFO] Task started: fastANI
[2023-03-17 23:54:21,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg554813a7-9675-485f-a0d2-cb361a17a6bd/OceanDNA-b41615.fa --refList OceanDNA-b41615/target_genomes.txt --output OceanDNA-b41615/fastani_result.tsv --threads 1
[2023-03-17 23:54:37,985] [INFO] Task succeeded: fastANI
[2023-03-17 23:54:37,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca77d718-0d8c-4c14-87f2-0372d34bb219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:54:37,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca77d718-0d8c-4c14-87f2-0372d34bb219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:54:37,986] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:54:37,986] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:54:37,986] [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
--------------------------------------------------------------------------------
[2023-03-17 23:54:37,988] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41615/tc_result.tsv
[2023-03-17 23:54:37,994] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:54:37,994] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:54:37,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca77d718-0d8c-4c14-87f2-0372d34bb219/dqc_reference/checkm_data
[2023-03-17 23:54:37,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:54:38,004] [INFO] Task started: CheckM
[2023-03-17 23:54:38,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41615/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41615/checkm_input OceanDNA-b41615/checkm_result
[2023-03-17 23:55:05,558] [INFO] Task succeeded: CheckM
[2023-03-17 23:55:05,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:55:05,576] [INFO] ===== Completeness check finished =====
[2023-03-17 23:55:05,576] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:55:05,577] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41615/markers.fasta)
[2023-03-17 23:55:05,577] [INFO] Task started: Blastn
[2023-03-17 23:55:05,578] [INFO] Running command: blastn -query OceanDNA-b41615/markers.fasta -db /var/lib/cwl/stgca77d718-0d8c-4c14-87f2-0372d34bb219/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41615/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:55:06,489] [INFO] Task succeeded: Blastn
[2023-03-17 23:55:06,494] [INFO] Selected 19 target genomes.
[2023-03-17 23:55:06,494] [INFO] Target genome list was writen to OceanDNA-b41615/target_genomes_gtdb.txt
[2023-03-17 23:55:06,513] [INFO] Task started: fastANI
[2023-03-17 23:55:06,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg554813a7-9675-485f-a0d2-cb361a17a6bd/OceanDNA-b41615.fa --refList OceanDNA-b41615/target_genomes_gtdb.txt --output OceanDNA-b41615/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:55:15,910] [INFO] Task succeeded: fastANI
[2023-03-17 23:55:15,915] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:55:15,915] [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_018668095.1	s__UBA7434 sp018668095	99.4908	480	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	98.20	98.20	0.79	0.79	2	conclusive
GCA_003492055.1	s__UBA7434 sp003492055	86.2293	274	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	98.70	98.70	0.91	0.91	2	-
GCA_905480475.1	s__UBA7434 sp905480475	77.6448	114	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336035.1	s__UBA7434 sp002336035	77.4461	52	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726445.1	s__UBA7434 sp002726445	76.7839	52	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.17	99.17	0.72	0.72	2	-
GCA_002339085.1	s__UBA7434 sp002339085	76.738	65	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.78	99.78	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:55:15,917] [INFO] GTDB search result was written to OceanDNA-b41615/result_gtdb.tsv
[2023-03-17 23:55:15,920] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:55:15,924] [INFO] DFAST_QC result json was written to OceanDNA-b41615/dqc_result.json
[2023-03-17 23:55:15,924] [INFO] DFAST_QC completed!
[2023-03-17 23:55:15,924] [INFO] Total running time: 0h1m5s