[2023-03-19 00:19:08,860] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:19:08,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:19:08,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg96ec5753-2c50-4948-a1c8-50579d32ceae/dqc_reference
[2023-03-19 00:19:10,373] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:19:10,373] [INFO] Task started: Prodigal
[2023-03-19 00:19:10,374] [INFO] Running command: cat /var/lib/cwl/stg48898d45-3a8d-4339-b5a3-a382d9c1ec78/OceanDNA-b1480.fa | prodigal -d OceanDNA-b1480/cds.fna -a OceanDNA-b1480/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:19:24,212] [INFO] Task succeeded: Prodigal
[2023-03-19 00:19:24,212] [INFO] Task started: HMMsearch
[2023-03-19 00:19:24,212] [INFO] Running command: hmmsearch --tblout OceanDNA-b1480/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96ec5753-2c50-4948-a1c8-50579d32ceae/dqc_reference/reference_markers.hmm OceanDNA-b1480/protein.faa > /dev/null
[2023-03-19 00:19:24,370] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:19:24,371] [INFO] Found 6/6 markers.
[2023-03-19 00:19:24,386] [INFO] Query marker FASTA was written to OceanDNA-b1480/markers.fasta
[2023-03-19 00:19:24,387] [INFO] Task started: Blastn
[2023-03-19 00:19:24,387] [INFO] Running command: blastn -query OceanDNA-b1480/markers.fasta -db /var/lib/cwl/stg96ec5753-2c50-4948-a1c8-50579d32ceae/dqc_reference/reference_markers.fasta -out OceanDNA-b1480/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:24,892] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:24,893] [INFO] Selected 16 target genomes.
[2023-03-19 00:19:24,893] [INFO] Target genome list was writen to OceanDNA-b1480/target_genomes.txt
[2023-03-19 00:19:24,903] [INFO] Task started: fastANI
[2023-03-19 00:19:24,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg48898d45-3a8d-4339-b5a3-a382d9c1ec78/OceanDNA-b1480.fa --refList OceanDNA-b1480/target_genomes.txt --output OceanDNA-b1480/fastani_result.tsv --threads 1
[2023-03-19 00:19:32,996] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:32,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96ec5753-2c50-4948-a1c8-50579d32ceae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:19:32,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96ec5753-2c50-4948-a1c8-50579d32ceae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:19:32,997] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:19:32,997] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:19:32,997] [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
--------------------------------------------------------------------------------
[2023-03-19 00:19:32,997] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1480/tc_result.tsv
[2023-03-19 00:19:32,997] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:19:32,997] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:19:32,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96ec5753-2c50-4948-a1c8-50579d32ceae/dqc_reference/checkm_data
[2023-03-19 00:19:33,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:19:33,004] [INFO] Task started: CheckM
[2023-03-19 00:19:33,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1480/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1480/checkm_input OceanDNA-b1480/checkm_result
[2023-03-19 00:20:10,722] [INFO] Task succeeded: CheckM
[2023-03-19 00:20:10,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:20:10,725] [INFO] ===== Completeness check finished =====
[2023-03-19 00:20:10,725] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:20:10,725] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1480/markers.fasta)
[2023-03-19 00:20:10,726] [INFO] Task started: Blastn
[2023-03-19 00:20:10,726] [INFO] Running command: blastn -query OceanDNA-b1480/markers.fasta -db /var/lib/cwl/stg96ec5753-2c50-4948-a1c8-50579d32ceae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1480/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:20:11,454] [INFO] Task succeeded: Blastn
[2023-03-19 00:20:11,455] [INFO] Selected 9 target genomes.
[2023-03-19 00:20:11,455] [INFO] Target genome list was writen to OceanDNA-b1480/target_genomes_gtdb.txt
[2023-03-19 00:20:11,466] [INFO] Task started: fastANI
[2023-03-19 00:20:11,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg48898d45-3a8d-4339-b5a3-a382d9c1ec78/OceanDNA-b1480.fa --refList OceanDNA-b1480/target_genomes_gtdb.txt --output OceanDNA-b1480/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:20:15,787] [INFO] Task succeeded: fastANI
[2023-03-19 00:20:15,792] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:20:15,792] [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_012960315.1	s__UBA2110 sp012960315	96.2183	701	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	99.85	99.85	0.95	0.95	2	conclusive
GCA_002331465.1	s__UBA2110 sp002331465	93.2008	554	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239555.1	s__UBA2110 sp014239555	88.6299	710	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719335.1	s__UBA2110 sp002719335	83.9608	527	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	96.75	96.75	0.83	0.83	2	-
GCA_002388005.1	s__UBA2110 sp002388005	79.0333	346	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705305.1	s__UBA2110 sp002705305	77.9123	321	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722565.1	s__MedAcidi-G3 sp002722565	76.4249	97	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	96.30	96.09	0.94	0.94	4	-
GCA_002724355.1	s__UBA6944 sp002724355	76.3199	67	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	98.32	97.68	0.80	0.76	5	-
--------------------------------------------------------------------------------
[2023-03-19 00:20:15,792] [INFO] GTDB search result was written to OceanDNA-b1480/result_gtdb.tsv
[2023-03-19 00:20:15,793] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:20:15,793] [INFO] DFAST_QC result json was written to OceanDNA-b1480/dqc_result.json
[2023-03-19 00:20:15,794] [INFO] DFAST_QC completed!
[2023-03-19 00:20:15,794] [INFO] Total running time: 0h1m7s