[2023-03-18 00:28:55,433] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:28:55,433] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:28:55,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg6db69473-9bcd-46cc-8720-9c4eef4211fe/dqc_reference
[2023-03-18 00:28:56,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:28:56,514] [INFO] Task started: Prodigal
[2023-03-18 00:28:56,514] [INFO] Running command: cat /var/lib/cwl/stg12eb2c1d-d12e-4a49-a1bc-ea044f9e0b4e/OceanDNA-b13082.fa | prodigal -d OceanDNA-b13082/cds.fna -a OceanDNA-b13082/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:29:12,043] [INFO] Task succeeded: Prodigal
[2023-03-18 00:29:12,044] [INFO] Task started: HMMsearch
[2023-03-18 00:29:12,044] [INFO] Running command: hmmsearch --tblout OceanDNA-b13082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6db69473-9bcd-46cc-8720-9c4eef4211fe/dqc_reference/reference_markers.hmm OceanDNA-b13082/protein.faa > /dev/null
[2023-03-18 00:29:12,220] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:29:12,220] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg12eb2c1d-d12e-4a49-a1bc-ea044f9e0b4e/OceanDNA-b13082.fa]
[2023-03-18 00:29:12,240] [INFO] Query marker FASTA was written to OceanDNA-b13082/markers.fasta
[2023-03-18 00:29:12,241] [INFO] Task started: Blastn
[2023-03-18 00:29:12,241] [INFO] Running command: blastn -query OceanDNA-b13082/markers.fasta -db /var/lib/cwl/stg6db69473-9bcd-46cc-8720-9c4eef4211fe/dqc_reference/reference_markers.fasta -out OceanDNA-b13082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:12,870] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:12,870] [INFO] Selected 21 target genomes.
[2023-03-18 00:29:12,871] [INFO] Target genome list was writen to OceanDNA-b13082/target_genomes.txt
[2023-03-18 00:29:12,879] [INFO] Task started: fastANI
[2023-03-18 00:29:12,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg12eb2c1d-d12e-4a49-a1bc-ea044f9e0b4e/OceanDNA-b13082.fa --refList OceanDNA-b13082/target_genomes.txt --output OceanDNA-b13082/fastani_result.tsv --threads 1
[2023-03-18 00:29:28,871] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:28,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6db69473-9bcd-46cc-8720-9c4eef4211fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:29:28,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6db69473-9bcd-46cc-8720-9c4eef4211fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:29:28,879] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:29:28,879] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:29:28,879] [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
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	80.5467	391	498	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	76.8252	170	498	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.4104	81	498	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	74.7503	131	498	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	74.7221	132	498	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	74.72	78	498	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	74.7143	134	498	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.669	59	498	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	74.6228	128	498	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	74.6004	106	498	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:29:28,879] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13082/tc_result.tsv
[2023-03-18 00:29:28,879] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:29:28,880] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:29:28,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6db69473-9bcd-46cc-8720-9c4eef4211fe/dqc_reference/checkm_data
[2023-03-18 00:29:28,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:29:28,900] [INFO] Task started: CheckM
[2023-03-18 00:29:28,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13082/checkm_input OceanDNA-b13082/checkm_result
[2023-03-18 00:30:09,883] [INFO] Task succeeded: CheckM
[2023-03-18 00:30:09,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:30:09,886] [INFO] ===== Completeness check finished =====
[2023-03-18 00:30:09,886] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:30:09,886] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13082/markers.fasta)
[2023-03-18 00:30:09,887] [INFO] Task started: Blastn
[2023-03-18 00:30:09,887] [INFO] Running command: blastn -query OceanDNA-b13082/markers.fasta -db /var/lib/cwl/stg6db69473-9bcd-46cc-8720-9c4eef4211fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:30:10,950] [INFO] Task succeeded: Blastn
[2023-03-18 00:30:10,950] [INFO] Selected 7 target genomes.
[2023-03-18 00:30:10,950] [INFO] Target genome list was writen to OceanDNA-b13082/target_genomes_gtdb.txt
[2023-03-18 00:30:10,972] [INFO] Task started: fastANI
[2023-03-18 00:30:10,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg12eb2c1d-d12e-4a49-a1bc-ea044f9e0b4e/OceanDNA-b13082.fa --refList OceanDNA-b13082/target_genomes_gtdb.txt --output OceanDNA-b13082/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:30:15,709] [INFO] Task succeeded: fastANI
[2023-03-18 00:30:15,714] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:30:15,714] [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_002283365.1	s__Rubrivirga marina	80.5172	393	498	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	80.0574	288	498	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	79.1556	333	498	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCA_012960515.1	s__Rubricoccus sp012960515	77.0814	190	498	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	76.8392	169	498	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003465.1	s__JABDIZ01 sp013003465	76.6038	91	498	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908885.1	s__JAAAOL01 sp009908885	75.6041	67	498	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:30:15,715] [INFO] GTDB search result was written to OceanDNA-b13082/result_gtdb.tsv
[2023-03-18 00:30:15,715] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:30:15,716] [INFO] DFAST_QC result json was written to OceanDNA-b13082/dqc_result.json
[2023-03-18 00:30:15,716] [INFO] DFAST_QC completed!
[2023-03-18 00:30:15,716] [INFO] Total running time: 0h1m20s