[2023-03-18 23:40:00,435] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c1bee1d-64de-48b7-b6e5-a3cc1ac1c46d/dqc_reference
[2023-03-18 23:40:01,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,558] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,559] [INFO] Running command: cat /var/lib/cwl/stg1a96e1ca-24ae-4dba-bae8-97abfedb8787/OceanDNA-b27603.fa | prodigal -d OceanDNA-b27603/cds.fna -a OceanDNA-b27603/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:10,386] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:10,386] [INFO] Task started: HMMsearch
[2023-03-18 23:40:10,386] [INFO] Running command: hmmsearch --tblout OceanDNA-b27603/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c1bee1d-64de-48b7-b6e5-a3cc1ac1c46d/dqc_reference/reference_markers.hmm OceanDNA-b27603/protein.faa > /dev/null
[2023-03-18 23:40:10,552] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:10,552] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1a96e1ca-24ae-4dba-bae8-97abfedb8787/OceanDNA-b27603.fa]
[2023-03-18 23:40:10,566] [INFO] Query marker FASTA was written to OceanDNA-b27603/markers.fasta
[2023-03-18 23:40:10,567] [INFO] Task started: Blastn
[2023-03-18 23:40:10,568] [INFO] Running command: blastn -query OceanDNA-b27603/markers.fasta -db /var/lib/cwl/stg6c1bee1d-64de-48b7-b6e5-a3cc1ac1c46d/dqc_reference/reference_markers.fasta -out OceanDNA-b27603/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:11,201] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:11,202] [INFO] Selected 27 target genomes.
[2023-03-18 23:40:11,203] [INFO] Target genome list was writen to OceanDNA-b27603/target_genomes.txt
[2023-03-18 23:40:11,218] [INFO] Task started: fastANI
[2023-03-18 23:40:11,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a96e1ca-24ae-4dba-bae8-97abfedb8787/OceanDNA-b27603.fa --refList OceanDNA-b27603/target_genomes.txt --output OceanDNA-b27603/fastani_result.tsv --threads 1
[2023-03-18 23:40:27,496] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:27,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c1bee1d-64de-48b7-b6e5-a3cc1ac1c46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:27,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c1bee1d-64de-48b7-b6e5-a3cc1ac1c46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:27,502] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:40:27,502] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:40:27,502] [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
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.1402	82	433	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.1364	59	433	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.0433	62	433	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	75.9536	64	433	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	75.9184	53	433	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	75.9004	74	433	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	75.8636	53	433	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:40:27,503] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27603/tc_result.tsv
[2023-03-18 23:40:27,503] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:27,503] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:27,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c1bee1d-64de-48b7-b6e5-a3cc1ac1c46d/dqc_reference/checkm_data
[2023-03-18 23:40:27,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:27,507] [INFO] Task started: CheckM
[2023-03-18 23:40:27,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27603/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27603/checkm_input OceanDNA-b27603/checkm_result
[2023-03-18 23:40:54,529] [INFO] Task succeeded: CheckM
[2023-03-18 23:40:54,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:40:54,531] [INFO] ===== Completeness check finished =====
[2023-03-18 23:40:54,531] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:40:54,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27603/markers.fasta)
[2023-03-18 23:40:54,532] [INFO] Task started: Blastn
[2023-03-18 23:40:54,532] [INFO] Running command: blastn -query OceanDNA-b27603/markers.fasta -db /var/lib/cwl/stg6c1bee1d-64de-48b7-b6e5-a3cc1ac1c46d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27603/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:55,590] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:55,591] [INFO] Selected 14 target genomes.
[2023-03-18 23:40:55,591] [INFO] Target genome list was writen to OceanDNA-b27603/target_genomes_gtdb.txt
[2023-03-18 23:40:55,604] [INFO] Task started: fastANI
[2023-03-18 23:40:55,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a96e1ca-24ae-4dba-bae8-97abfedb8787/OceanDNA-b27603.fa --refList OceanDNA-b27603/target_genomes_gtdb.txt --output OceanDNA-b27603/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:41:02,852] [INFO] Task succeeded: fastANI
[2023-03-18 23:41:02,859] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:41:02,860] [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_015693905.1	s__M30B80 sp015693905	96.9941	417	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__M30B80	95.0	97.47	96.18	0.91	0.87	8	conclusive
GCA_015689775.1	s__M30B80 sp015689775	93.4366	418	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__M30B80	95.0	99.19	99.19	0.96	0.96	2	-
GCA_018401385.1	s__M30B80 sp018401385	81.8904	296	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__M30B80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402035.1	s__Roseicyclus sp018402035	76.8302	107	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	76.7564	68	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689735.1	s__Roseicyclus sp015689735	76.6878	83	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004751985.1	s__Rhodophyticola sp004751985	76.2827	83	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	76.1402	82	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401965.1	s__Roseicyclus sp018401965	76.1052	80	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	75.9536	64	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001879715.1	s__Nioella nitratireducens	75.9184	53	433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:41:02,860] [INFO] GTDB search result was written to OceanDNA-b27603/result_gtdb.tsv
[2023-03-18 23:41:02,860] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:41:02,861] [INFO] DFAST_QC result json was written to OceanDNA-b27603/dqc_result.json
[2023-03-18 23:41:02,861] [INFO] DFAST_QC completed!
[2023-03-18 23:41:02,861] [INFO] Total running time: 0h1m2s