[2023-03-18 20:59:43,926] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg58f5ed28-d93b-4561-ad9e-040246e2c4e8/dqc_reference
[2023-03-18 20:59:45,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,685] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,685] [INFO] Running command: cat /var/lib/cwl/stge5c01db0-a970-4c32-8a14-6c920f3dfeba/OceanDNA-b37783.fa | prodigal -d OceanDNA-b37783/cds.fna -a OceanDNA-b37783/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:58,993] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:58,993] [INFO] Task started: HMMsearch
[2023-03-18 20:59:58,993] [INFO] Running command: hmmsearch --tblout OceanDNA-b37783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58f5ed28-d93b-4561-ad9e-040246e2c4e8/dqc_reference/reference_markers.hmm OceanDNA-b37783/protein.faa > /dev/null
[2023-03-18 20:59:59,187] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:59,188] [INFO] Found 6/6 markers.
[2023-03-18 20:59:59,205] [INFO] Query marker FASTA was written to OceanDNA-b37783/markers.fasta
[2023-03-18 20:59:59,205] [INFO] Task started: Blastn
[2023-03-18 20:59:59,205] [INFO] Running command: blastn -query OceanDNA-b37783/markers.fasta -db /var/lib/cwl/stg58f5ed28-d93b-4561-ad9e-040246e2c4e8/dqc_reference/reference_markers.fasta -out OceanDNA-b37783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:59,808] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:59,810] [INFO] Selected 27 target genomes.
[2023-03-18 20:59:59,810] [INFO] Target genome list was writen to OceanDNA-b37783/target_genomes.txt
[2023-03-18 20:59:59,822] [INFO] Task started: fastANI
[2023-03-18 20:59:59,822] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c01db0-a970-4c32-8a14-6c920f3dfeba/OceanDNA-b37783.fa --refList OceanDNA-b37783/target_genomes.txt --output OceanDNA-b37783/fastani_result.tsv --threads 1
[2023-03-18 21:00:15,736] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:15,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58f5ed28-d93b-4561-ad9e-040246e2c4e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:15,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58f5ed28-d93b-4561-ad9e-040246e2c4e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:15,737] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:15,737] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:00:15,737] [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 21:00:15,737] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37783/tc_result.tsv
[2023-03-18 21:00:15,737] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:15,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:15,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58f5ed28-d93b-4561-ad9e-040246e2c4e8/dqc_reference/checkm_data
[2023-03-18 21:00:15,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:15,779] [INFO] Task started: CheckM
[2023-03-18 21:00:15,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37783/checkm_input OceanDNA-b37783/checkm_result
[2023-03-18 21:00:52,856] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:52,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:52,879] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:52,879] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:52,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37783/markers.fasta)
[2023-03-18 21:00:52,880] [INFO] Task started: Blastn
[2023-03-18 21:00:52,881] [INFO] Running command: blastn -query OceanDNA-b37783/markers.fasta -db /var/lib/cwl/stg58f5ed28-d93b-4561-ad9e-040246e2c4e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:53,822] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:53,829] [INFO] Selected 15 target genomes.
[2023-03-18 21:00:53,829] [INFO] Target genome list was writen to OceanDNA-b37783/target_genomes_gtdb.txt
[2023-03-18 21:00:53,839] [INFO] Task started: fastANI
[2023-03-18 21:00:53,839] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c01db0-a970-4c32-8a14-6c920f3dfeba/OceanDNA-b37783.fa --refList OceanDNA-b37783/target_genomes_gtdb.txt --output OceanDNA-b37783/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:00,222] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:00,226] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:01:00,226] [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_905182485.1	s__Luminiphilus sp905182485	92.7202	505	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666055.1	s__Luminiphilus sp018666055	87.8946	311	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478845.1	s__Luminiphilus sp905478845	86.2082	524	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683335.1	s__Luminiphilus sp002683335	78.4868	58	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.43	98.43	0.60	0.60	2	-
GCA_002683395.1	s__Luminiphilus sp002683395	76.7814	86	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	-
GCA_002721785.1	s__Luminiphilus sp002721785	76.2437	80	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:00,230] [INFO] GTDB search result was written to OceanDNA-b37783/result_gtdb.tsv
[2023-03-18 21:01:00,231] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:00,231] [INFO] DFAST_QC result json was written to OceanDNA-b37783/dqc_result.json
[2023-03-18 21:01:00,231] [INFO] DFAST_QC completed!
[2023-03-18 21:01:00,232] [INFO] Total running time: 0h1m16s