[2023-03-15 04:59:01,521] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:59:01,521] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:59:01,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg828dae87-21cd-4d22-af04-ce637c232009/dqc_reference
[2023-03-15 04:59:03,420] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:59:03,421] [INFO] Task started: Prodigal
[2023-03-15 04:59:03,422] [INFO] Running command: cat /var/lib/cwl/stg32c04c18-46ea-4b8c-bdf6-4725b20a2908/OceanDNA-b26433.fa | prodigal -d OceanDNA-b26433/cds.fna -a OceanDNA-b26433/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:59:16,907] [INFO] Task succeeded: Prodigal
[2023-03-15 04:59:16,908] [INFO] Task started: HMMsearch
[2023-03-15 04:59:16,908] [INFO] Running command: hmmsearch --tblout OceanDNA-b26433/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg828dae87-21cd-4d22-af04-ce637c232009/dqc_reference/reference_markers.hmm OceanDNA-b26433/protein.faa > /dev/null
[2023-03-15 04:59:17,093] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:59:17,093] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32c04c18-46ea-4b8c-bdf6-4725b20a2908/OceanDNA-b26433.fa]
[2023-03-15 04:59:17,118] [INFO] Query marker FASTA was written to OceanDNA-b26433/markers.fasta
[2023-03-15 04:59:17,119] [INFO] Task started: Blastn
[2023-03-15 04:59:17,119] [INFO] Running command: blastn -query OceanDNA-b26433/markers.fasta -db /var/lib/cwl/stg828dae87-21cd-4d22-af04-ce637c232009/dqc_reference/reference_markers.fasta -out OceanDNA-b26433/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:59:17,788] [INFO] Task succeeded: Blastn
[2023-03-15 04:59:17,793] [INFO] Selected 26 target genomes.
[2023-03-15 04:59:17,793] [INFO] Target genome list was writen to OceanDNA-b26433/target_genomes.txt
[2023-03-15 04:59:17,810] [INFO] Task started: fastANI
[2023-03-15 04:59:17,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c04c18-46ea-4b8c-bdf6-4725b20a2908/OceanDNA-b26433.fa --refList OceanDNA-b26433/target_genomes.txt --output OceanDNA-b26433/fastani_result.tsv --threads 1
[2023-03-15 04:59:42,969] [INFO] Task succeeded: fastANI
[2023-03-15 04:59:42,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg828dae87-21cd-4d22-af04-ce637c232009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:59:42,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg828dae87-21cd-4d22-af04-ce637c232009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:59:42,974] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:59:42,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:59:42,975] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.841	52	713	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.8277	51	713	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.3146	51	713	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.1745	50	713	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.1745	50	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:59:42,976] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26433/tc_result.tsv
[2023-03-15 04:59:42,978] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:59:42,978] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:59:42,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg828dae87-21cd-4d22-af04-ce637c232009/dqc_reference/checkm_data
[2023-03-15 04:59:42,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:59:42,998] [INFO] Task started: CheckM
[2023-03-15 04:59:42,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26433/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26433/checkm_input OceanDNA-b26433/checkm_result
[2023-03-15 05:00:20,752] [INFO] Task succeeded: CheckM
[2023-03-15 05:00:20,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:00:20,835] [INFO] ===== Completeness check finished =====
[2023-03-15 05:00:20,835] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:00:20,835] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26433/markers.fasta)
[2023-03-15 05:00:20,836] [INFO] Task started: Blastn
[2023-03-15 05:00:20,836] [INFO] Running command: blastn -query OceanDNA-b26433/markers.fasta -db /var/lib/cwl/stg828dae87-21cd-4d22-af04-ce637c232009/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26433/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:21,875] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:21,879] [INFO] Selected 15 target genomes.
[2023-03-15 05:00:21,879] [INFO] Target genome list was writen to OceanDNA-b26433/target_genomes_gtdb.txt
[2023-03-15 05:00:21,897] [INFO] Task started: fastANI
[2023-03-15 05:00:21,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c04c18-46ea-4b8c-bdf6-4725b20a2908/OceanDNA-b26433.fa --refList OceanDNA-b26433/target_genomes_gtdb.txt --output OceanDNA-b26433/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:00:30,449] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:30,454] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:00:30,454] [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_004213025.1	s__UBA8309 sp004213025	81.4714	232	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920665.1	s__UBA8309 sp009920665	81.1439	471	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	80.9151	452	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	79.1267	336	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	78.3397	229	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	77.2038	141	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_011524735.1	s__UBA8309 sp011524735	77.0685	136	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	75.8277	51	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:00:30,455] [INFO] GTDB search result was written to OceanDNA-b26433/result_gtdb.tsv
[2023-03-15 05:00:30,456] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:00:30,458] [INFO] DFAST_QC result json was written to OceanDNA-b26433/dqc_result.json
[2023-03-15 05:00:30,458] [INFO] DFAST_QC completed!
[2023-03-15 05:00:30,458] [INFO] Total running time: 0h1m29s