[2023-03-16 16:16:25,425] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:16:25,425] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:16:25,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fca0b24-a4a0-4a9c-a095-288a9492669d/dqc_reference
[2023-03-16 16:16:26,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:16:26,607] [INFO] Task started: Prodigal
[2023-03-16 16:16:26,608] [INFO] Running command: cat /var/lib/cwl/stga3178f37-fef0-4289-bdd9-1250ef1131a5/OceanDNA-b29390.fa | prodigal -d OceanDNA-b29390/cds.fna -a OceanDNA-b29390/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:16:41,706] [INFO] Task succeeded: Prodigal
[2023-03-16 16:16:41,706] [INFO] Task started: HMMsearch
[2023-03-16 16:16:41,706] [INFO] Running command: hmmsearch --tblout OceanDNA-b29390/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fca0b24-a4a0-4a9c-a095-288a9492669d/dqc_reference/reference_markers.hmm OceanDNA-b29390/protein.faa > /dev/null
[2023-03-16 16:16:41,874] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:16:41,874] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga3178f37-fef0-4289-bdd9-1250ef1131a5/OceanDNA-b29390.fa]
[2023-03-16 16:16:41,888] [INFO] Query marker FASTA was written to OceanDNA-b29390/markers.fasta
[2023-03-16 16:16:41,888] [INFO] Task started: Blastn
[2023-03-16 16:16:41,888] [INFO] Running command: blastn -query OceanDNA-b29390/markers.fasta -db /var/lib/cwl/stg7fca0b24-a4a0-4a9c-a095-288a9492669d/dqc_reference/reference_markers.fasta -out OceanDNA-b29390/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:16:42,864] [INFO] Task succeeded: Blastn
[2023-03-16 16:16:42,865] [INFO] Selected 23 target genomes.
[2023-03-16 16:16:42,865] [INFO] Target genome list was writen to OceanDNA-b29390/target_genomes.txt
[2023-03-16 16:16:42,878] [INFO] Task started: fastANI
[2023-03-16 16:16:42,878] [INFO] Running command: fastANI --query /var/lib/cwl/stga3178f37-fef0-4289-bdd9-1250ef1131a5/OceanDNA-b29390.fa --refList OceanDNA-b29390/target_genomes.txt --output OceanDNA-b29390/fastani_result.tsv --threads 1
[2023-03-16 16:16:57,630] [INFO] Task succeeded: fastANI
[2023-03-16 16:16:57,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fca0b24-a4a0-4a9c-a095-288a9492669d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:16:57,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fca0b24-a4a0-4a9c-a095-288a9492669d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:16:57,643] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:16:57,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:16:57,643] [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
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	79.885	358	503	95	below_threshold
Jannaschia aquimarina	strain=GSW-M26	GCA_000877395.1	935700	935700	type	True	78.8549	285	503	95	below_threshold
Jannaschia aquimarina	strain=DSM 28248	GCA_900188045.1	935700	935700	type	True	78.8497	282	503	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	78.7787	307	503	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	78.7787	307	503	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	78.7182	282	503	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	78.6367	284	503	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.3254	278	503	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.9345	246	503	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	77.8446	256	503	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.3957	188	503	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	77.3637	227	503	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	77.2988	229	503	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.2694	192	503	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.2507	155	503	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	77.083	193	503	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	77.0786	196	503	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0559	196	503	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.9292	204	503	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.7152	129	503	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.5363	111	503	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.2726	186	503	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.1089	131	503	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:16:57,644] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29390/tc_result.tsv
[2023-03-16 16:16:57,644] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:16:57,644] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:16:57,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fca0b24-a4a0-4a9c-a095-288a9492669d/dqc_reference/checkm_data
[2023-03-16 16:16:57,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:16:57,647] [INFO] Task started: CheckM
[2023-03-16 16:16:57,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29390/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29390/checkm_input OceanDNA-b29390/checkm_result
[2023-03-16 16:17:22,931] [INFO] Task succeeded: CheckM
[2023-03-16 16:17:22,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:17:22,933] [INFO] ===== Completeness check finished =====
[2023-03-16 16:17:22,934] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:17:22,934] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29390/markers.fasta)
[2023-03-16 16:17:22,935] [INFO] Task started: Blastn
[2023-03-16 16:17:22,935] [INFO] Running command: blastn -query OceanDNA-b29390/markers.fasta -db /var/lib/cwl/stg7fca0b24-a4a0-4a9c-a095-288a9492669d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29390/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:17:24,176] [INFO] Task succeeded: Blastn
[2023-03-16 16:17:24,177] [INFO] Selected 16 target genomes.
[2023-03-16 16:17:24,177] [INFO] Target genome list was writen to OceanDNA-b29390/target_genomes_gtdb.txt
[2023-03-16 16:17:24,339] [INFO] Task started: fastANI
[2023-03-16 16:17:24,339] [INFO] Running command: fastANI --query /var/lib/cwl/stga3178f37-fef0-4289-bdd9-1250ef1131a5/OceanDNA-b29390.fa --refList OceanDNA-b29390/target_genomes_gtdb.txt --output OceanDNA-b29390/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:17:34,915] [INFO] Task succeeded: fastANI
[2023-03-16 16:17:34,925] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:17:34,925] [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_016820245.1	s__Jannaschia sp016820245	81.1633	387	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	79.8123	363	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	78.8807	303	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000877395.1	s__Jannaschia aquimarina	78.8393	286	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900116765.1	s__Jannaschia seohaensis	78.8001	305	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.671	304	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	78.6512	283	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000153305.1	s__Oceanicola granulosus	78.3353	284	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.3128	279	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	78.2123	226	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	77.9932	259	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.9317	246	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	77.9296	284	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	77.8408	257	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.7637	263	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.5653	249	503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:17:34,926] [INFO] GTDB search result was written to OceanDNA-b29390/result_gtdb.tsv
[2023-03-16 16:17:34,926] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:17:34,928] [INFO] DFAST_QC result json was written to OceanDNA-b29390/dqc_result.json
[2023-03-16 16:17:34,928] [INFO] DFAST_QC completed!
[2023-03-16 16:17:34,928] [INFO] Total running time: 0h1m10s