[2023-03-15 07:58:33,366] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:58:33,367] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:58:33,368] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1c88254-a8a7-4830-9c4a-118db541b24b/dqc_reference
[2023-03-15 07:58:35,140] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:58:35,140] [INFO] Task started: Prodigal
[2023-03-15 07:58:35,140] [INFO] Running command: cat /var/lib/cwl/stg378c6fea-226e-4273-9cd8-1d378f8eefc7/OceanDNA-b4007.fa | prodigal -d OceanDNA-b4007/cds.fna -a OceanDNA-b4007/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:59:18,193] [INFO] Task succeeded: Prodigal
[2023-03-15 07:59:18,193] [INFO] Task started: HMMsearch
[2023-03-15 07:59:18,193] [INFO] Running command: hmmsearch --tblout OceanDNA-b4007/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1c88254-a8a7-4830-9c4a-118db541b24b/dqc_reference/reference_markers.hmm OceanDNA-b4007/protein.faa > /dev/null
[2023-03-15 07:59:18,448] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:59:18,449] [INFO] Found 6/6 markers.
[2023-03-15 07:59:18,504] [INFO] Query marker FASTA was written to OceanDNA-b4007/markers.fasta
[2023-03-15 07:59:18,505] [INFO] Task started: Blastn
[2023-03-15 07:59:18,505] [INFO] Running command: blastn -query OceanDNA-b4007/markers.fasta -db /var/lib/cwl/stgf1c88254-a8a7-4830-9c4a-118db541b24b/dqc_reference/reference_markers.fasta -out OceanDNA-b4007/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:59:19,053] [INFO] Task succeeded: Blastn
[2023-03-15 07:59:19,086] [INFO] Selected 13 target genomes.
[2023-03-15 07:59:19,087] [INFO] Target genome list was writen to OceanDNA-b4007/target_genomes.txt
[2023-03-15 07:59:19,095] [INFO] Task started: fastANI
[2023-03-15 07:59:19,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg378c6fea-226e-4273-9cd8-1d378f8eefc7/OceanDNA-b4007.fa --refList OceanDNA-b4007/target_genomes.txt --output OceanDNA-b4007/fastani_result.tsv --threads 1
[2023-03-15 07:59:31,867] [INFO] Task succeeded: fastANI
[2023-03-15 07:59:31,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1c88254-a8a7-4830-9c4a-118db541b24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:59:31,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1c88254-a8a7-4830-9c4a-118db541b24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:59:31,874] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:59:31,874] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:59:31,874] [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
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	87.6644	1651	2011	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	87.6419	1628	2011	95	below_threshold
Cyclobacterium amurskyense	strain=KCTC 12363	GCA_001050135.1	320787	320787	type	True	82.4204	1436	2011	95	below_threshold
Cyclobacterium marinum	strain=DSM 745	GCA_000222485.1	104	104	type	True	80.4954	1056	2011	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	77.4217	249	2011	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	77.2952	286	2011	95	below_threshold
Litoribacter populi	strain=XAAS-A1	GCA_007483685.1	2598460	2598460	type	True	76.1332	76	2011	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:59:31,877] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4007/tc_result.tsv
[2023-03-15 07:59:31,879] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:59:31,879] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:59:31,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1c88254-a8a7-4830-9c4a-118db541b24b/dqc_reference/checkm_data
[2023-03-15 07:59:31,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:59:31,890] [INFO] Task started: CheckM
[2023-03-15 07:59:31,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4007/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4007/checkm_input OceanDNA-b4007/checkm_result
[2023-03-15 08:01:15,344] [INFO] Task succeeded: CheckM
[2023-03-15 08:01:15,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:01:15,466] [INFO] ===== Completeness check finished =====
[2023-03-15 08:01:15,466] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:01:15,466] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4007/markers.fasta)
[2023-03-15 08:01:15,467] [INFO] Task started: Blastn
[2023-03-15 08:01:15,468] [INFO] Running command: blastn -query OceanDNA-b4007/markers.fasta -db /var/lib/cwl/stgf1c88254-a8a7-4830-9c4a-118db541b24b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4007/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:01:16,216] [INFO] Task succeeded: Blastn
[2023-03-15 08:01:16,223] [INFO] Selected 16 target genomes.
[2023-03-15 08:01:16,223] [INFO] Target genome list was writen to OceanDNA-b4007/target_genomes_gtdb.txt
[2023-03-15 08:01:16,241] [INFO] Task started: fastANI
[2023-03-15 08:01:16,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg378c6fea-226e-4273-9cd8-1d378f8eefc7/OceanDNA-b4007.fa --refList OceanDNA-b4007/target_genomes_gtdb.txt --output OceanDNA-b4007/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:01:30,964] [INFO] Task succeeded: fastANI
[2023-03-15 08:01:30,971] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:01:30,972] [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_000427295.1	s__Cyclobacterium qasimii	87.6419	1628	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001050135.1	s__Cyclobacterium amurskyense	82.4195	1435	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222485.1	s__Cyclobacterium marinum	80.5045	1054	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	98.85	98.76	0.93	0.93	3	-
GCA_014762705.1	s__Cyclobacterium sp014762705	77.5091	298	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	77.4217	249	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	77.285	287	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018500185.1	s__Litoribacter ruber	76.5145	62	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_900112005.1	s__Algoriphagus aquimarinus	76.4763	67	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483685.1	s__Litoribacter sp007483685	76.1332	76	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	76.0924	53	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	75.4661	55	2011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:01:31,070] [INFO] GTDB search result was written to OceanDNA-b4007/result_gtdb.tsv
[2023-03-15 08:01:31,098] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:01:31,110] [INFO] DFAST_QC result json was written to OceanDNA-b4007/dqc_result.json
[2023-03-15 08:01:31,110] [INFO] DFAST_QC completed!
[2023-03-15 08:01:31,110] [INFO] Total running time: 0h2m58s