[2023-03-16 07:11:53,908] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:11:53,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:11:53,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgc20319e5-f964-4425-90d4-c85ca17db7af/dqc_reference
[2023-03-16 07:11:55,001] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:11:55,001] [INFO] Task started: Prodigal
[2023-03-16 07:11:55,001] [INFO] Running command: cat /var/lib/cwl/stg33c15712-b69d-4e2e-8cad-96bda5908caf/OceanDNA-b45831.fa | prodigal -d OceanDNA-b45831/cds.fna -a OceanDNA-b45831/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:12:28,403] [INFO] Task succeeded: Prodigal
[2023-03-16 07:12:28,403] [INFO] Task started: HMMsearch
[2023-03-16 07:12:28,403] [INFO] Running command: hmmsearch --tblout OceanDNA-b45831/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc20319e5-f964-4425-90d4-c85ca17db7af/dqc_reference/reference_markers.hmm OceanDNA-b45831/protein.faa > /dev/null
[2023-03-16 07:12:28,600] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:12:28,600] [INFO] Found 6/6 markers.
[2023-03-16 07:12:28,638] [INFO] Query marker FASTA was written to OceanDNA-b45831/markers.fasta
[2023-03-16 07:12:28,640] [INFO] Task started: Blastn
[2023-03-16 07:12:28,640] [INFO] Running command: blastn -query OceanDNA-b45831/markers.fasta -db /var/lib/cwl/stgc20319e5-f964-4425-90d4-c85ca17db7af/dqc_reference/reference_markers.fasta -out OceanDNA-b45831/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:12:29,200] [INFO] Task succeeded: Blastn
[2023-03-16 07:12:29,205] [INFO] Selected 12 target genomes.
[2023-03-16 07:12:29,206] [INFO] Target genome list was writen to OceanDNA-b45831/target_genomes.txt
[2023-03-16 07:12:29,252] [INFO] Task started: fastANI
[2023-03-16 07:12:29,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c15712-b69d-4e2e-8cad-96bda5908caf/OceanDNA-b45831.fa --refList OceanDNA-b45831/target_genomes.txt --output OceanDNA-b45831/fastani_result.tsv --threads 1
[2023-03-16 07:12:38,103] [INFO] Task succeeded: fastANI
[2023-03-16 07:12:38,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc20319e5-f964-4425-90d4-c85ca17db7af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:12:38,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc20319e5-f964-4425-90d4-c85ca17db7af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:12:38,107] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:12:38,107] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:12:38,107] [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
Pelagicoccus mobilis	strain=KCTC 13126	GCA_016595505.1	415221	415221	type	True	76.5026	50	1401	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:12:38,108] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45831/tc_result.tsv
[2023-03-16 07:12:38,109] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:12:38,109] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:12:38,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc20319e5-f964-4425-90d4-c85ca17db7af/dqc_reference/checkm_data
[2023-03-16 07:12:38,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:12:38,191] [INFO] Task started: CheckM
[2023-03-16 07:12:38,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45831/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45831/checkm_input OceanDNA-b45831/checkm_result
[2023-03-16 07:13:59,132] [INFO] Task succeeded: CheckM
[2023-03-16 07:13:59,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:13:59,143] [INFO] ===== Completeness check finished =====
[2023-03-16 07:13:59,144] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:13:59,144] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45831/markers.fasta)
[2023-03-16 07:13:59,146] [INFO] Task started: Blastn
[2023-03-16 07:13:59,146] [INFO] Running command: blastn -query OceanDNA-b45831/markers.fasta -db /var/lib/cwl/stgc20319e5-f964-4425-90d4-c85ca17db7af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45831/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:14:00,090] [INFO] Task succeeded: Blastn
[2023-03-16 07:14:00,094] [INFO] Selected 18 target genomes.
[2023-03-16 07:14:00,094] [INFO] Target genome list was writen to OceanDNA-b45831/target_genomes_gtdb.txt
[2023-03-16 07:14:00,109] [INFO] Task started: fastANI
[2023-03-16 07:14:00,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c15712-b69d-4e2e-8cad-96bda5908caf/OceanDNA-b45831.fa --refList OceanDNA-b45831/target_genomes_gtdb.txt --output OceanDNA-b45831/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:14:09,718] [INFO] Task succeeded: fastANI
[2023-03-16 07:14:09,722] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:14:09,722] [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_002474325.1	s__UBA5691 sp002474325	88.1705	696	1401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	98.86	98.86	0.81	0.81	2	-
GCA_002694885.1	s__UBA5691 sp002694885	82.6102	720	1401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.79	99.79	0.86	0.86	2	-
GCA_014529625.1	s__UBA5691 sp002420265	78.3432	142	1401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	96.17	95.09	0.91	0.87	4	-
GCA_002420185.1	s__UBA5691 sp002420185	77.0409	85	1401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595505.1	s__Pelagicoccus mobilis	76.5026	50	1401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:14:09,723] [INFO] GTDB search result was written to OceanDNA-b45831/result_gtdb.tsv
[2023-03-16 07:14:09,723] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:14:09,725] [INFO] DFAST_QC result json was written to OceanDNA-b45831/dqc_result.json
[2023-03-16 07:14:09,725] [INFO] DFAST_QC completed!
[2023-03-16 07:14:09,725] [INFO] Total running time: 0h2m16s