[2023-03-17 10:35:02,805] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,806] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,806] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4487c4a-1600-484b-a84c-b62930ea4304/dqc_reference
[2023-03-17 10:35:04,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,550] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,550] [INFO] Running command: cat /var/lib/cwl/stg30eedaad-2c77-4b02-a2ed-1877b02bd699/OceanDNA-b26354.fa | prodigal -d OceanDNA-b26354/cds.fna -a OceanDNA-b26354/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:14,723] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:14,724] [INFO] Task started: HMMsearch
[2023-03-17 10:35:14,724] [INFO] Running command: hmmsearch --tblout OceanDNA-b26354/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4487c4a-1600-484b-a84c-b62930ea4304/dqc_reference/reference_markers.hmm OceanDNA-b26354/protein.faa > /dev/null
[2023-03-17 10:35:14,897] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:14,897] [INFO] Found 6/6 markers.
[2023-03-17 10:35:14,911] [INFO] Query marker FASTA was written to OceanDNA-b26354/markers.fasta
[2023-03-17 10:35:14,912] [INFO] Task started: Blastn
[2023-03-17 10:35:14,912] [INFO] Running command: blastn -query OceanDNA-b26354/markers.fasta -db /var/lib/cwl/stgb4487c4a-1600-484b-a84c-b62930ea4304/dqc_reference/reference_markers.fasta -out OceanDNA-b26354/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:15,465] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:15,466] [INFO] Selected 20 target genomes.
[2023-03-17 10:35:15,467] [INFO] Target genome list was writen to OceanDNA-b26354/target_genomes.txt
[2023-03-17 10:35:15,477] [INFO] Task started: fastANI
[2023-03-17 10:35:15,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg30eedaad-2c77-4b02-a2ed-1877b02bd699/OceanDNA-b26354.fa --refList OceanDNA-b26354/target_genomes.txt --output OceanDNA-b26354/fastani_result.tsv --threads 1
[2023-03-17 10:35:26,614] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:26,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4487c4a-1600-484b-a84c-b62930ea4304/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:26,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4487c4a-1600-484b-a84c-b62930ea4304/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:26,615] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:26,615] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:35:26,615] [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
--------------------------------------------------------------------------------
[2023-03-17 10:35:26,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26354/tc_result.tsv
[2023-03-17 10:35:26,616] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:26,616] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:26,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4487c4a-1600-484b-a84c-b62930ea4304/dqc_reference/checkm_data
[2023-03-17 10:35:26,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:26,623] [INFO] Task started: CheckM
[2023-03-17 10:35:26,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26354/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26354/checkm_input OceanDNA-b26354/checkm_result
[2023-03-17 10:35:56,082] [INFO] Task succeeded: CheckM
[2023-03-17 10:35:56,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:35:56,085] [INFO] ===== Completeness check finished =====
[2023-03-17 10:35:56,085] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:35:56,085] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26354/markers.fasta)
[2023-03-17 10:35:56,086] [INFO] Task started: Blastn
[2023-03-17 10:35:56,086] [INFO] Running command: blastn -query OceanDNA-b26354/markers.fasta -db /var/lib/cwl/stgb4487c4a-1600-484b-a84c-b62930ea4304/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26354/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:56,985] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:56,986] [INFO] Selected 19 target genomes.
[2023-03-17 10:35:56,986] [INFO] Target genome list was writen to OceanDNA-b26354/target_genomes_gtdb.txt
[2023-03-17 10:35:57,521] [INFO] Task started: fastANI
[2023-03-17 10:35:57,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg30eedaad-2c77-4b02-a2ed-1877b02bd699/OceanDNA-b26354.fa --refList OceanDNA-b26354/target_genomes_gtdb.txt --output OceanDNA-b26354/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:36:04,271] [INFO] Task succeeded: fastANI
[2023-03-17 10:36:04,275] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:36:04,275] [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_016779005.1	s__UBA5951 sp016779005	98.8069	550	612	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	96.62	95.51	0.89	0.87	4	conclusive
GCA_009936885.1	s__UBA5951 sp009936885	94.3989	354	612	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516825.1	s__UBA5951 sp902516825	86.3604	311	612	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666135.1	s__UBA5951 sp018666135	78.2053	202	612	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.32	99.32	0.87	0.87	2	-
GCA_012269555.1	s__UBA5951 sp012269555	77.3503	150	612	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:36:04,275] [INFO] GTDB search result was written to OceanDNA-b26354/result_gtdb.tsv
[2023-03-17 10:36:04,275] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:36:04,276] [INFO] DFAST_QC result json was written to OceanDNA-b26354/dqc_result.json
[2023-03-17 10:36:04,276] [INFO] DFAST_QC completed!
[2023-03-17 10:36:04,276] [INFO] Total running time: 0h1m1s