[2023-03-15 08:11:06,149] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:06,168] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:06,168] [INFO] DQC Reference Directory: /var/lib/cwl/stgeef57d82-5200-4464-9f24-86bcd0a77e86/dqc_reference
[2023-03-15 08:11:07,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,278] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,278] [INFO] Running command: cat /var/lib/cwl/stg697b3b1c-a302-48b4-ac0d-61a5f209d649/OceanDNA-b24309.fa | prodigal -d OceanDNA-b24309/cds.fna -a OceanDNA-b24309/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:20,895] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:20,896] [INFO] Task started: HMMsearch
[2023-03-15 08:11:20,896] [INFO] Running command: hmmsearch --tblout OceanDNA-b24309/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeef57d82-5200-4464-9f24-86bcd0a77e86/dqc_reference/reference_markers.hmm OceanDNA-b24309/protein.faa > /dev/null
[2023-03-15 08:11:21,092] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:21,092] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg697b3b1c-a302-48b4-ac0d-61a5f209d649/OceanDNA-b24309.fa]
[2023-03-15 08:11:21,141] [INFO] Query marker FASTA was written to OceanDNA-b24309/markers.fasta
[2023-03-15 08:11:21,141] [INFO] Task started: Blastn
[2023-03-15 08:11:21,141] [INFO] Running command: blastn -query OceanDNA-b24309/markers.fasta -db /var/lib/cwl/stgeef57d82-5200-4464-9f24-86bcd0a77e86/dqc_reference/reference_markers.fasta -out OceanDNA-b24309/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:21,757] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:21,806] [INFO] Selected 27 target genomes.
[2023-03-15 08:11:21,806] [INFO] Target genome list was writen to OceanDNA-b24309/target_genomes.txt
[2023-03-15 08:11:21,826] [INFO] Task started: fastANI
[2023-03-15 08:11:21,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg697b3b1c-a302-48b4-ac0d-61a5f209d649/OceanDNA-b24309.fa --refList OceanDNA-b24309/target_genomes.txt --output OceanDNA-b24309/fastani_result.tsv --threads 1
[2023-03-15 08:11:39,009] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:39,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeef57d82-5200-4464-9f24-86bcd0a77e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:39,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeef57d82-5200-4464-9f24-86bcd0a77e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:39,012] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:39,012] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:11:39,012] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.1916	54	619	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:11:39,021] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24309/tc_result.tsv
[2023-03-15 08:11:39,026] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:39,026] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:39,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeef57d82-5200-4464-9f24-86bcd0a77e86/dqc_reference/checkm_data
[2023-03-15 08:11:39,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:39,041] [INFO] Task started: CheckM
[2023-03-15 08:11:39,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24309/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24309/checkm_input OceanDNA-b24309/checkm_result
[2023-03-15 08:12:16,562] [INFO] Task succeeded: CheckM
[2023-03-15 08:12:16,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.72%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:12:16,566] [INFO] ===== Completeness check finished =====
[2023-03-15 08:12:16,566] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:12:16,566] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24309/markers.fasta)
[2023-03-15 08:12:16,567] [INFO] Task started: Blastn
[2023-03-15 08:12:16,567] [INFO] Running command: blastn -query OceanDNA-b24309/markers.fasta -db /var/lib/cwl/stgeef57d82-5200-4464-9f24-86bcd0a77e86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24309/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:17,532] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:17,546] [INFO] Selected 10 target genomes.
[2023-03-15 08:12:17,546] [INFO] Target genome list was writen to OceanDNA-b24309/target_genomes_gtdb.txt
[2023-03-15 08:12:17,578] [INFO] Task started: fastANI
[2023-03-15 08:12:17,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg697b3b1c-a302-48b4-ac0d-61a5f209d649/OceanDNA-b24309.fa --refList OceanDNA-b24309/target_genomes_gtdb.txt --output OceanDNA-b24309/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:12:24,278] [INFO] Task succeeded: fastANI
[2023-03-15 08:12:24,282] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:12:24,282] [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_016776605.1	s__GCA-2731375 sp016776605	95.484	579	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018701215.1	s__GCA-2731375 sp018701215	79.0609	417	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_018667855.1	s__GCA-2731375 sp018667855	78.6148	337	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_002731375.1	s__GCA-2731375 sp002731375	78.0995	305	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
GCA_018660265.1	s__GCA-2731375 sp018660265	77.8798	299	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
--------------------------------------------------------------------------------
[2023-03-15 08:12:24,282] [INFO] GTDB search result was written to OceanDNA-b24309/result_gtdb.tsv
[2023-03-15 08:12:24,282] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:12:24,283] [INFO] DFAST_QC result json was written to OceanDNA-b24309/dqc_result.json
[2023-03-15 08:12:24,283] [INFO] DFAST_QC completed!
[2023-03-15 08:12:24,284] [INFO] Total running time: 0h1m18s