[2023-03-18 21:29:09,885] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:29:09,885] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:29:09,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgc902df96-72b2-432b-ba7a-bd09ba1a12c9/dqc_reference
[2023-03-18 21:29:10,964] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:29:10,964] [INFO] Task started: Prodigal
[2023-03-18 21:29:10,964] [INFO] Running command: cat /var/lib/cwl/stg44741d87-6a0c-4a23-b09a-60ea6859dd76/OceanDNA-b24207.fa | prodigal -d OceanDNA-b24207/cds.fna -a OceanDNA-b24207/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:29:15,292] [INFO] Task succeeded: Prodigal
[2023-03-18 21:29:15,293] [INFO] Task started: HMMsearch
[2023-03-18 21:29:15,293] [INFO] Running command: hmmsearch --tblout OceanDNA-b24207/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc902df96-72b2-432b-ba7a-bd09ba1a12c9/dqc_reference/reference_markers.hmm OceanDNA-b24207/protein.faa > /dev/null
[2023-03-18 21:29:15,457] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:29:15,457] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg44741d87-6a0c-4a23-b09a-60ea6859dd76/OceanDNA-b24207.fa]
[2023-03-18 21:29:15,465] [INFO] Query marker FASTA was written to OceanDNA-b24207/markers.fasta
[2023-03-18 21:29:15,466] [INFO] Task started: Blastn
[2023-03-18 21:29:15,466] [INFO] Running command: blastn -query OceanDNA-b24207/markers.fasta -db /var/lib/cwl/stgc902df96-72b2-432b-ba7a-bd09ba1a12c9/dqc_reference/reference_markers.fasta -out OceanDNA-b24207/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:15,952] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:15,952] [INFO] Selected 10 target genomes.
[2023-03-18 21:29:15,953] [INFO] Target genome list was writen to OceanDNA-b24207/target_genomes.txt
[2023-03-18 21:29:15,959] [INFO] Task started: fastANI
[2023-03-18 21:29:15,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg44741d87-6a0c-4a23-b09a-60ea6859dd76/OceanDNA-b24207.fa --refList OceanDNA-b24207/target_genomes.txt --output OceanDNA-b24207/fastani_result.tsv --threads 1
[2023-03-18 21:29:19,857] [INFO] Task succeeded: fastANI
[2023-03-18 21:29:19,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc902df96-72b2-432b-ba7a-bd09ba1a12c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:29:19,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc902df96-72b2-432b-ba7a-bd09ba1a12c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:29:19,858] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:29:19,858] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:29:19,858] [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
--------------------------------------------------------------------------------
[2023-03-18 21:29:19,858] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24207/tc_result.tsv
[2023-03-18 21:29:19,858] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:29:19,858] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:29:19,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc902df96-72b2-432b-ba7a-bd09ba1a12c9/dqc_reference/checkm_data
[2023-03-18 21:29:19,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:29:19,898] [INFO] Task started: CheckM
[2023-03-18 21:29:19,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24207/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24207/checkm_input OceanDNA-b24207/checkm_result
[2023-03-18 21:29:37,005] [INFO] Task succeeded: CheckM
[2023-03-18 21:29:37,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.65%
Contamintation: 2.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:29:37,008] [INFO] ===== Completeness check finished =====
[2023-03-18 21:29:37,008] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:29:37,008] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24207/markers.fasta)
[2023-03-18 21:29:37,009] [INFO] Task started: Blastn
[2023-03-18 21:29:37,010] [INFO] Running command: blastn -query OceanDNA-b24207/markers.fasta -db /var/lib/cwl/stgc902df96-72b2-432b-ba7a-bd09ba1a12c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24207/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:37,640] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:37,641] [INFO] Selected 15 target genomes.
[2023-03-18 21:29:37,642] [INFO] Target genome list was writen to OceanDNA-b24207/target_genomes_gtdb.txt
[2023-03-18 21:29:37,653] [INFO] Task started: fastANI
[2023-03-18 21:29:37,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg44741d87-6a0c-4a23-b09a-60ea6859dd76/OceanDNA-b24207.fa --refList OceanDNA-b24207/target_genomes_gtdb.txt --output OceanDNA-b24207/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:29:41,226] [INFO] Task succeeded: fastANI
[2023-03-18 21:29:41,230] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:29:41,230] [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_002711715.1	s__GCA-002720895 sp002711715	94.4488	114	239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607475.1	s__GCA-002720895 sp902607475	87.3399	154	239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937775.1	s__GCA-002720895 sp002937775	80.7989	155	239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.14	99.14	0.75	0.75	2	-
GCA_002717245.1	s__GCA-002720895 sp002717245	80.4967	202	239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.29	99.29	0.96	0.96	2	-
GCA_002720895.1	s__GCA-002720895 sp002720895	79.7486	125	239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:29:41,231] [INFO] GTDB search result was written to OceanDNA-b24207/result_gtdb.tsv
[2023-03-18 21:29:41,231] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:29:41,233] [INFO] DFAST_QC result json was written to OceanDNA-b24207/dqc_result.json
[2023-03-18 21:29:41,233] [INFO] DFAST_QC completed!
[2023-03-18 21:29:41,233] [INFO] Total running time: 0h0m31s