[2023-03-16 00:13:32,301] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:13:32,301] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:13:32,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgae10ea96-3e70-4bf6-b6ae-5105c38ebed2/dqc_reference
[2023-03-16 00:13:33,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:13:33,470] [INFO] Task started: Prodigal
[2023-03-16 00:13:33,470] [INFO] Running command: cat /var/lib/cwl/stg08e216ae-5ea7-416a-9d40-030445dbdb68/OceanDNA-b4959.fa | prodigal -d OceanDNA-b4959/cds.fna -a OceanDNA-b4959/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:13:38,979] [INFO] Task succeeded: Prodigal
[2023-03-16 00:13:38,979] [INFO] Task started: HMMsearch
[2023-03-16 00:13:38,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b4959/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae10ea96-3e70-4bf6-b6ae-5105c38ebed2/dqc_reference/reference_markers.hmm OceanDNA-b4959/protein.faa > /dev/null
[2023-03-16 00:13:39,120] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:13:39,121] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg08e216ae-5ea7-416a-9d40-030445dbdb68/OceanDNA-b4959.fa]
[2023-03-16 00:13:39,134] [INFO] Query marker FASTA was written to OceanDNA-b4959/markers.fasta
[2023-03-16 00:13:39,136] [INFO] Task started: Blastn
[2023-03-16 00:13:39,136] [INFO] Running command: blastn -query OceanDNA-b4959/markers.fasta -db /var/lib/cwl/stgae10ea96-3e70-4bf6-b6ae-5105c38ebed2/dqc_reference/reference_markers.fasta -out OceanDNA-b4959/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:13:39,669] [INFO] Task succeeded: Blastn
[2023-03-16 00:13:39,671] [INFO] Selected 32 target genomes.
[2023-03-16 00:13:39,671] [INFO] Target genome list was writen to OceanDNA-b4959/target_genomes.txt
[2023-03-16 00:13:39,688] [INFO] Task started: fastANI
[2023-03-16 00:13:39,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg08e216ae-5ea7-416a-9d40-030445dbdb68/OceanDNA-b4959.fa --refList OceanDNA-b4959/target_genomes.txt --output OceanDNA-b4959/fastani_result.tsv --threads 1
[2023-03-16 00:13:56,238] [INFO] Task succeeded: fastANI
[2023-03-16 00:13:56,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae10ea96-3e70-4bf6-b6ae-5105c38ebed2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:13:56,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae10ea96-3e70-4bf6-b6ae-5105c38ebed2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:13:56,239] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:13:56,239] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:13:56,239] [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 00:13:56,241] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4959/tc_result.tsv
[2023-03-16 00:13:56,243] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:13:56,244] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:13:56,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae10ea96-3e70-4bf6-b6ae-5105c38ebed2/dqc_reference/checkm_data
[2023-03-16 00:13:56,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:13:56,254] [INFO] Task started: CheckM
[2023-03-16 00:13:56,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4959/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4959/checkm_input OceanDNA-b4959/checkm_result
[2023-03-16 00:14:16,313] [INFO] Task succeeded: CheckM
[2023-03-16 00:14:16,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.50%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:14:16,337] [INFO] ===== Completeness check finished =====
[2023-03-16 00:14:16,337] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:14:16,338] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4959/markers.fasta)
[2023-03-16 00:14:16,339] [INFO] Task started: Blastn
[2023-03-16 00:14:16,339] [INFO] Running command: blastn -query OceanDNA-b4959/markers.fasta -db /var/lib/cwl/stgae10ea96-3e70-4bf6-b6ae-5105c38ebed2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4959/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:14:17,095] [INFO] Task succeeded: Blastn
[2023-03-16 00:14:17,099] [INFO] Selected 25 target genomes.
[2023-03-16 00:14:17,099] [INFO] Target genome list was writen to OceanDNA-b4959/target_genomes_gtdb.txt
[2023-03-16 00:14:17,124] [INFO] Task started: fastANI
[2023-03-16 00:14:17,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg08e216ae-5ea7-416a-9d40-030445dbdb68/OceanDNA-b4959.fa --refList OceanDNA-b4959/target_genomes_gtdb.txt --output OceanDNA-b4959/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:14:23,776] [INFO] Task succeeded: fastANI
[2023-03-16 00:14:23,779] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:14:23,780] [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_002696275.1	s__GCA-002697625 sp002696275	80.0192	136	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697625.1	s__GCA-002697625 sp002697625	78.014	88	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478555.1	s__GCA-002697625 sp905478555	76.7035	61	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_018647945.1	s__GCA-002697625 sp018647945	76.414	54	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-16 00:14:23,782] [INFO] GTDB search result was written to OceanDNA-b4959/result_gtdb.tsv
[2023-03-16 00:14:23,784] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:14:23,786] [INFO] DFAST_QC result json was written to OceanDNA-b4959/dqc_result.json
[2023-03-16 00:14:23,786] [INFO] DFAST_QC completed!
[2023-03-16 00:14:23,786] [INFO] Total running time: 0h0m51s