[2023-03-18 09:58:36,588] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,588] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg45595093-5035-4344-8e1e-7e5ca88bd2ff/dqc_reference
[2023-03-18 09:58:38,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,404] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,404] [INFO] Running command: cat /var/lib/cwl/stgebc5bb36-531b-4282-86a7-9566859e69ff/OceanDNA-b34113.fa | prodigal -d OceanDNA-b34113/cds.fna -a OceanDNA-b34113/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:58:43,339] [INFO] Task succeeded: Prodigal
[2023-03-18 09:58:43,340] [INFO] Task started: HMMsearch
[2023-03-18 09:58:43,340] [INFO] Running command: hmmsearch --tblout OceanDNA-b34113/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45595093-5035-4344-8e1e-7e5ca88bd2ff/dqc_reference/reference_markers.hmm OceanDNA-b34113/protein.faa > /dev/null
[2023-03-18 09:58:43,510] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:58:43,510] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgebc5bb36-531b-4282-86a7-9566859e69ff/OceanDNA-b34113.fa]
[2023-03-18 09:58:43,521] [INFO] Query marker FASTA was written to OceanDNA-b34113/markers.fasta
[2023-03-18 09:58:43,523] [INFO] Task started: Blastn
[2023-03-18 09:58:43,523] [INFO] Running command: blastn -query OceanDNA-b34113/markers.fasta -db /var/lib/cwl/stg45595093-5035-4344-8e1e-7e5ca88bd2ff/dqc_reference/reference_markers.fasta -out OceanDNA-b34113/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:58:44,880] [INFO] Task succeeded: Blastn
[2023-03-18 09:58:44,881] [INFO] Selected 30 target genomes.
[2023-03-18 09:58:44,881] [INFO] Target genome list was writen to OceanDNA-b34113/target_genomes.txt
[2023-03-18 09:58:44,924] [INFO] Task started: fastANI
[2023-03-18 09:58:44,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc5bb36-531b-4282-86a7-9566859e69ff/OceanDNA-b34113.fa --refList OceanDNA-b34113/target_genomes.txt --output OceanDNA-b34113/fastani_result.tsv --threads 1
[2023-03-18 09:59:03,304] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:03,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45595093-5035-4344-8e1e-7e5ca88bd2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:59:03,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45595093-5035-4344-8e1e-7e5ca88bd2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:59:03,305] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:59:03,305] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:59:03,305] [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 09:59:03,305] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34113/tc_result.tsv
[2023-03-18 09:59:03,306] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:59:03,306] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:59:03,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45595093-5035-4344-8e1e-7e5ca88bd2ff/dqc_reference/checkm_data
[2023-03-18 09:59:03,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:59:03,312] [INFO] Task started: CheckM
[2023-03-18 09:59:03,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34113/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34113/checkm_input OceanDNA-b34113/checkm_result
[2023-03-18 09:59:21,923] [INFO] Task succeeded: CheckM
[2023-03-18 09:59:21,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:59:21,925] [INFO] ===== Completeness check finished =====
[2023-03-18 09:59:21,926] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:59:21,926] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34113/markers.fasta)
[2023-03-18 09:59:21,926] [INFO] Task started: Blastn
[2023-03-18 09:59:21,926] [INFO] Running command: blastn -query OceanDNA-b34113/markers.fasta -db /var/lib/cwl/stg45595093-5035-4344-8e1e-7e5ca88bd2ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34113/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:22,647] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:22,648] [INFO] Selected 20 target genomes.
[2023-03-18 09:59:22,648] [INFO] Target genome list was writen to OceanDNA-b34113/target_genomes_gtdb.txt
[2023-03-18 09:59:22,670] [INFO] Task started: fastANI
[2023-03-18 09:59:22,670] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc5bb36-531b-4282-86a7-9566859e69ff/OceanDNA-b34113.fa --refList OceanDNA-b34113/target_genomes_gtdb.txt --output OceanDNA-b34113/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:59:29,822] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:29,826] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:59:29,826] [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_002721545.1	s__GCA-2721545 sp002721545	99.7243	306	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	99.74	99.74	0.93	0.93	2	conclusive
GCA_014237605.1	s__GCA-2721545 sp014237605	80.1192	203	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	95.61	95.61	0.87	0.87	2	-
GCA_905612245.1	s__GCA-2721545 sp905612245	80.0545	159	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003230615.1	s__GCA-2721545 sp003230615	76.509	61	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	97.47	97.47	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:59:29,826] [INFO] GTDB search result was written to OceanDNA-b34113/result_gtdb.tsv
[2023-03-18 09:59:29,827] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:59:29,827] [INFO] DFAST_QC result json was written to OceanDNA-b34113/dqc_result.json
[2023-03-18 09:59:29,827] [INFO] DFAST_QC completed!
[2023-03-18 09:59:29,827] [INFO] Total running time: 0h0m53s