[2023-03-18 09:42:02,231] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:42:02,231] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:42:02,231] [INFO] DQC Reference Directory: /var/lib/cwl/stgcce2ef12-8221-4a15-a6b0-b469768cfd21/dqc_reference
[2023-03-18 09:42:03,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:42:03,347] [INFO] Task started: Prodigal
[2023-03-18 09:42:03,347] [INFO] Running command: cat /var/lib/cwl/stg2f6ffc35-2272-438c-b0ca-e1edac12670e/OceanDNA-b30065.fa | prodigal -d OceanDNA-b30065/cds.fna -a OceanDNA-b30065/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:42:14,561] [INFO] Task succeeded: Prodigal
[2023-03-18 09:42:14,562] [INFO] Task started: HMMsearch
[2023-03-18 09:42:14,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b30065/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcce2ef12-8221-4a15-a6b0-b469768cfd21/dqc_reference/reference_markers.hmm OceanDNA-b30065/protein.faa > /dev/null
[2023-03-18 09:42:14,708] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:42:14,709] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2f6ffc35-2272-438c-b0ca-e1edac12670e/OceanDNA-b30065.fa]
[2023-03-18 09:42:14,729] [INFO] Query marker FASTA was written to OceanDNA-b30065/markers.fasta
[2023-03-18 09:42:14,730] [INFO] Task started: Blastn
[2023-03-18 09:42:14,730] [INFO] Running command: blastn -query OceanDNA-b30065/markers.fasta -db /var/lib/cwl/stgcce2ef12-8221-4a15-a6b0-b469768cfd21/dqc_reference/reference_markers.fasta -out OceanDNA-b30065/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:15,240] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:15,241] [INFO] Selected 15 target genomes.
[2023-03-18 09:42:15,241] [INFO] Target genome list was writen to OceanDNA-b30065/target_genomes.txt
[2023-03-18 09:42:15,249] [INFO] Task started: fastANI
[2023-03-18 09:42:15,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f6ffc35-2272-438c-b0ca-e1edac12670e/OceanDNA-b30065.fa --refList OceanDNA-b30065/target_genomes.txt --output OceanDNA-b30065/fastani_result.tsv --threads 1
[2023-03-18 09:42:24,334] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:24,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcce2ef12-8221-4a15-a6b0-b469768cfd21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:42:24,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcce2ef12-8221-4a15-a6b0-b469768cfd21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:42:24,339] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:42:24,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:42:24,339] [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
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	77.0872	98	464	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	77.0715	97	464	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	76.698	73	464	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.6869	59	464	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.6869	59	464	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:42:24,340] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30065/tc_result.tsv
[2023-03-18 09:42:24,340] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:42:24,340] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:42:24,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcce2ef12-8221-4a15-a6b0-b469768cfd21/dqc_reference/checkm_data
[2023-03-18 09:42:24,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:42:24,351] [INFO] Task started: CheckM
[2023-03-18 09:42:24,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30065/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30065/checkm_input OceanDNA-b30065/checkm_result
[2023-03-18 09:42:56,820] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:56,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:56,823] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:56,823] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:56,823] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30065/markers.fasta)
[2023-03-18 09:42:56,824] [INFO] Task started: Blastn
[2023-03-18 09:42:56,824] [INFO] Running command: blastn -query OceanDNA-b30065/markers.fasta -db /var/lib/cwl/stgcce2ef12-8221-4a15-a6b0-b469768cfd21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30065/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:57,780] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:57,781] [INFO] Selected 19 target genomes.
[2023-03-18 09:42:57,781] [INFO] Target genome list was writen to OceanDNA-b30065/target_genomes_gtdb.txt
[2023-03-18 09:42:57,796] [INFO] Task started: fastANI
[2023-03-18 09:42:57,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f6ffc35-2272-438c-b0ca-e1edac12670e/OceanDNA-b30065.fa --refList OceanDNA-b30065/target_genomes_gtdb.txt --output OceanDNA-b30065/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:43:10,091] [INFO] Task succeeded: fastANI
[2023-03-18 09:43:10,096] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:43:10,096] [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
GCF_000014045.1	s__Roseobacter denitrificans	77.0872	98	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009811755.1	s__Roseobacter cerasinus	76.698	73	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.6869	59	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_015644665.1	s__Roseobacter sp015644665	76.3397	94	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	76.294	51	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	75.9531	61	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	75.6811	55	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:43:10,096] [INFO] GTDB search result was written to OceanDNA-b30065/result_gtdb.tsv
[2023-03-18 09:43:10,096] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:43:10,097] [INFO] DFAST_QC result json was written to OceanDNA-b30065/dqc_result.json
[2023-03-18 09:43:10,097] [INFO] DFAST_QC completed!
[2023-03-18 09:43:10,097] [INFO] Total running time: 0h1m8s