[2023-03-17 01:44:57,151] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,151] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg3edc943c-9ecc-41b4-8f9c-0d7a6120ba7d/dqc_reference
[2023-03-17 01:44:59,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:44:59,094] [INFO] Task started: Prodigal
[2023-03-17 01:44:59,094] [INFO] Running command: cat /var/lib/cwl/stg03a59298-ed2c-4d4f-8fdb-34620190adf6/OceanDNA-b7395.fa | prodigal -d OceanDNA-b7395/cds.fna -a OceanDNA-b7395/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:07,089] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:07,089] [INFO] Task started: HMMsearch
[2023-03-17 01:45:07,089] [INFO] Running command: hmmsearch --tblout OceanDNA-b7395/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3edc943c-9ecc-41b4-8f9c-0d7a6120ba7d/dqc_reference/reference_markers.hmm OceanDNA-b7395/protein.faa > /dev/null
[2023-03-17 01:45:07,259] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:07,260] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg03a59298-ed2c-4d4f-8fdb-34620190adf6/OceanDNA-b7395.fa]
[2023-03-17 01:45:07,270] [INFO] Query marker FASTA was written to OceanDNA-b7395/markers.fasta
[2023-03-17 01:45:07,270] [INFO] Task started: Blastn
[2023-03-17 01:45:07,270] [INFO] Running command: blastn -query OceanDNA-b7395/markers.fasta -db /var/lib/cwl/stg3edc943c-9ecc-41b4-8f9c-0d7a6120ba7d/dqc_reference/reference_markers.fasta -out OceanDNA-b7395/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:07,849] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:07,850] [INFO] Selected 30 target genomes.
[2023-03-17 01:45:07,850] [INFO] Target genome list was writen to OceanDNA-b7395/target_genomes.txt
[2023-03-17 01:45:07,870] [INFO] Task started: fastANI
[2023-03-17 01:45:07,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg03a59298-ed2c-4d4f-8fdb-34620190adf6/OceanDNA-b7395.fa --refList OceanDNA-b7395/target_genomes.txt --output OceanDNA-b7395/fastani_result.tsv --threads 1
[2023-03-17 01:45:24,945] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:24,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3edc943c-9ecc-41b4-8f9c-0d7a6120ba7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:24,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3edc943c-9ecc-41b4-8f9c-0d7a6120ba7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:24,950] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:24,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:45:24,950] [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
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	75.9702	53	411	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	75.8337	50	411	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	75.6691	52	411	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	75.3349	56	411	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:45:24,950] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7395/tc_result.tsv
[2023-03-17 01:45:24,950] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:24,950] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:24,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3edc943c-9ecc-41b4-8f9c-0d7a6120ba7d/dqc_reference/checkm_data
[2023-03-17 01:45:24,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:24,953] [INFO] Task started: CheckM
[2023-03-17 01:45:24,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7395/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7395/checkm_input OceanDNA-b7395/checkm_result
[2023-03-17 01:45:49,822] [INFO] Task succeeded: CheckM
[2023-03-17 01:45:49,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 01:45:49,824] [INFO] ===== Completeness check finished =====
[2023-03-17 01:45:49,824] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:45:49,824] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7395/markers.fasta)
[2023-03-17 01:45:49,825] [INFO] Task started: Blastn
[2023-03-17 01:45:49,826] [INFO] Running command: blastn -query OceanDNA-b7395/markers.fasta -db /var/lib/cwl/stg3edc943c-9ecc-41b4-8f9c-0d7a6120ba7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7395/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:50,647] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:50,648] [INFO] Selected 11 target genomes.
[2023-03-17 01:45:50,648] [INFO] Target genome list was writen to OceanDNA-b7395/target_genomes_gtdb.txt
[2023-03-17 01:45:50,835] [INFO] Task started: fastANI
[2023-03-17 01:45:50,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg03a59298-ed2c-4d4f-8fdb-34620190adf6/OceanDNA-b7395.fa --refList OceanDNA-b7395/target_genomes_gtdb.txt --output OceanDNA-b7395/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:45:54,884] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:54,890] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:45:54,891] [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_905181825.1	s__Hel1-33-131 sp905181825	89.6261	326	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	82.725	320	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	79.3705	254	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	78.8364	220	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	78.5103	195	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	78.4249	214	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	78.3992	217	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	78.3978	184	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	78.0966	158	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:45:54,891] [INFO] GTDB search result was written to OceanDNA-b7395/result_gtdb.tsv
[2023-03-17 01:45:54,891] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:45:54,892] [INFO] DFAST_QC result json was written to OceanDNA-b7395/dqc_result.json
[2023-03-17 01:45:54,892] [INFO] DFAST_QC completed!
[2023-03-17 01:45:54,892] [INFO] Total running time: 0h0m58s