[2023-03-19 04:46:19,986] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:19,987] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:19,987] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbf83e39-1ba6-4351-bfc7-29bf44948f32/dqc_reference
[2023-03-19 04:46:21,109] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:21,109] [INFO] Task started: Prodigal
[2023-03-19 04:46:21,110] [INFO] Running command: cat /var/lib/cwl/stg8e473626-7f44-4fd2-96bc-37b1efe3a6c6/OceanDNA-b26476.fa | prodigal -d OceanDNA-b26476/cds.fna -a OceanDNA-b26476/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:35,641] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:35,641] [INFO] Task started: HMMsearch
[2023-03-19 04:46:35,641] [INFO] Running command: hmmsearch --tblout OceanDNA-b26476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbf83e39-1ba6-4351-bfc7-29bf44948f32/dqc_reference/reference_markers.hmm OceanDNA-b26476/protein.faa > /dev/null
[2023-03-19 04:46:35,822] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:35,823] [INFO] Found 6/6 markers.
[2023-03-19 04:46:35,840] [INFO] Query marker FASTA was written to OceanDNA-b26476/markers.fasta
[2023-03-19 04:46:35,840] [INFO] Task started: Blastn
[2023-03-19 04:46:35,840] [INFO] Running command: blastn -query OceanDNA-b26476/markers.fasta -db /var/lib/cwl/stgfbf83e39-1ba6-4351-bfc7-29bf44948f32/dqc_reference/reference_markers.fasta -out OceanDNA-b26476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:36,566] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:36,567] [INFO] Selected 31 target genomes.
[2023-03-19 04:46:36,567] [INFO] Target genome list was writen to OceanDNA-b26476/target_genomes.txt
[2023-03-19 04:46:36,582] [INFO] Task started: fastANI
[2023-03-19 04:46:36,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e473626-7f44-4fd2-96bc-37b1efe3a6c6/OceanDNA-b26476.fa --refList OceanDNA-b26476/target_genomes.txt --output OceanDNA-b26476/fastani_result.tsv --threads 1
[2023-03-19 04:46:55,752] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:55,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbf83e39-1ba6-4351-bfc7-29bf44948f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:55,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbf83e39-1ba6-4351-bfc7-29bf44948f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:55,761] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:55,762] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:46:55,762] [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
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.4252	91	755	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4144	88	755	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.3567	58	755	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.3213	86	755	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.217	83	755	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	76.007	65	755	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.9868	65	755	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	75.9514	57	755	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.9385	51	755	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	75.9373	56	755	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.7523	81	755	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.7252	57	755	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.7252	57	755	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.7251	57	755	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.5709	74	755	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:46:55,762] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26476/tc_result.tsv
[2023-03-19 04:46:55,762] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:55,762] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:55,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbf83e39-1ba6-4351-bfc7-29bf44948f32/dqc_reference/checkm_data
[2023-03-19 04:46:55,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:46:55,767] [INFO] Task started: CheckM
[2023-03-19 04:46:55,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26476/checkm_input OceanDNA-b26476/checkm_result
[2023-03-19 04:47:36,422] [INFO] Task succeeded: CheckM
[2023-03-19 04:47:36,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:47:36,425] [INFO] ===== Completeness check finished =====
[2023-03-19 04:47:36,425] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:47:36,425] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26476/markers.fasta)
[2023-03-19 04:47:36,425] [INFO] Task started: Blastn
[2023-03-19 04:47:36,425] [INFO] Running command: blastn -query OceanDNA-b26476/markers.fasta -db /var/lib/cwl/stgfbf83e39-1ba6-4351-bfc7-29bf44948f32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:47:37,757] [INFO] Task succeeded: Blastn
[2023-03-19 04:47:37,758] [INFO] Selected 14 target genomes.
[2023-03-19 04:47:37,758] [INFO] Target genome list was writen to OceanDNA-b26476/target_genomes_gtdb.txt
[2023-03-19 04:47:37,769] [INFO] Task started: fastANI
[2023-03-19 04:47:37,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e473626-7f44-4fd2-96bc-37b1efe3a6c6/OceanDNA-b26476.fa --refList OceanDNA-b26476/target_genomes_gtdb.txt --output OceanDNA-b26476/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:47:44,150] [INFO] Task succeeded: fastANI
[2023-03-19 04:47:44,158] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:47:44,158] [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_002457745.1	s__UBA8309 sp002457745	99.3405	465	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011522725.1	s__UBA8309 sp001627655	81.376	472	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_009920665.1	s__UBA8309 sp009920665	80.011	428	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	79.9655	430	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	79.0216	204	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_016780765.1	s__UBA8309 sp016780765	78.0621	229	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_011524735.1	s__UBA8309 sp011524735	77.7216	192	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547925.1	s__MED-G116 sp902547925	77.2871	59	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	76.9765	144	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936825.1	s__UBA8309 sp009936825	76.3463	92	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	75.9252	58	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCA_017859295.1	s__UBA3439 sp017859295	75.7205	51	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCF_900172365.1	s__Roseovarius gaetbuli	75.4756	50	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:47:44,158] [INFO] GTDB search result was written to OceanDNA-b26476/result_gtdb.tsv
[2023-03-19 04:47:44,159] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:47:44,160] [INFO] DFAST_QC result json was written to OceanDNA-b26476/dqc_result.json
[2023-03-19 04:47:44,160] [INFO] DFAST_QC completed!
[2023-03-19 04:47:44,160] [INFO] Total running time: 0h1m24s