[2023-03-18 07:06:20,016] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,016] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,016] [INFO] DQC Reference Directory: /var/lib/cwl/stg70bd9e44-7213-4acc-aac9-d811ab6da333/dqc_reference
[2023-03-18 07:06:21,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:21,104] [INFO] Task started: Prodigal
[2023-03-18 07:06:21,104] [INFO] Running command: cat /var/lib/cwl/stg83f182f6-ff71-400a-bc9a-a1596bd9d89c/OceanDNA-b23460.fa | prodigal -d OceanDNA-b23460/cds.fna -a OceanDNA-b23460/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:40,900] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:40,900] [INFO] Task started: HMMsearch
[2023-03-18 07:06:40,900] [INFO] Running command: hmmsearch --tblout OceanDNA-b23460/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70bd9e44-7213-4acc-aac9-d811ab6da333/dqc_reference/reference_markers.hmm OceanDNA-b23460/protein.faa > /dev/null
[2023-03-18 07:06:41,109] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:41,109] [INFO] Found 6/6 markers.
[2023-03-18 07:06:41,129] [INFO] Query marker FASTA was written to OceanDNA-b23460/markers.fasta
[2023-03-18 07:06:41,129] [INFO] Task started: Blastn
[2023-03-18 07:06:41,129] [INFO] Running command: blastn -query OceanDNA-b23460/markers.fasta -db /var/lib/cwl/stg70bd9e44-7213-4acc-aac9-d811ab6da333/dqc_reference/reference_markers.fasta -out OceanDNA-b23460/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:42,072] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:42,073] [INFO] Selected 16 target genomes.
[2023-03-18 07:06:42,073] [INFO] Target genome list was writen to OceanDNA-b23460/target_genomes.txt
[2023-03-18 07:06:42,081] [INFO] Task started: fastANI
[2023-03-18 07:06:42,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg83f182f6-ff71-400a-bc9a-a1596bd9d89c/OceanDNA-b23460.fa --refList OceanDNA-b23460/target_genomes.txt --output OceanDNA-b23460/fastani_result.tsv --threads 1
[2023-03-18 07:06:57,939] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:57,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70bd9e44-7213-4acc-aac9-d811ab6da333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:57,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70bd9e44-7213-4acc-aac9-d811ab6da333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:57,949] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:57,949] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:57,949] [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
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	81.0431	677	1113	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	81.0186	676	1113	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	80.8389	612	1113	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	80.2629	618	1113	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	80.1708	613	1113	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.144	593	1113	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	79.6123	448	1113	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.4246	557	1113	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.1987	566	1113	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	79.1595	581	1113	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	79.0518	588	1113	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	79.0185	582	1113	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	78.948	583	1113	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	78.9435	594	1113	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.0435	275	1113	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.7776	193	1113	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:57,949] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23460/tc_result.tsv
[2023-03-18 07:06:57,949] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:57,949] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:57,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70bd9e44-7213-4acc-aac9-d811ab6da333/dqc_reference/checkm_data
[2023-03-18 07:06:57,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:57,955] [INFO] Task started: CheckM
[2023-03-18 07:06:57,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23460/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23460/checkm_input OceanDNA-b23460/checkm_result
[2023-03-18 07:07:47,181] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:47,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:47,184] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:47,184] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:47,184] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23460/markers.fasta)
[2023-03-18 07:07:47,184] [INFO] Task started: Blastn
[2023-03-18 07:07:47,185] [INFO] Running command: blastn -query OceanDNA-b23460/markers.fasta -db /var/lib/cwl/stg70bd9e44-7213-4acc-aac9-d811ab6da333/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23460/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:48,978] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:48,979] [INFO] Selected 17 target genomes.
[2023-03-18 07:07:48,979] [INFO] Target genome list was writen to OceanDNA-b23460/target_genomes_gtdb.txt
[2023-03-18 07:07:49,248] [INFO] Task started: fastANI
[2023-03-18 07:07:49,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg83f182f6-ff71-400a-bc9a-a1596bd9d89c/OceanDNA-b23460.fa --refList OceanDNA-b23460/target_genomes_gtdb.txt --output OceanDNA-b23460/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:08:04,399] [INFO] Task succeeded: fastANI
[2023-03-18 07:08:04,409] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:08:04,409] [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_002363865.1	s__Phenylobacterium sp002363865	87.6554	899	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCA_002441055.1	s__Phenylobacterium sp002441055	86.0628	650	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	84.5458	865	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_018001015.1	s__Phenylobacterium sp018001015	81.0126	647	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCF_003254505.1	s__Phenylobacterium hankyongense	80.8912	607	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240795.1	s__Phenylobacterium sp018240795	80.5294	596	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425305.1	s__Phenylobacterium sp001425305	80.3833	636	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000017265.1	s__Phenylobacterium zucineum	80.2671	618	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_004799515.1	s__Phenylobacterium sp004799515	80.2552	577	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254475.1	s__Phenylobacterium soli	80.2019	586	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822795.1	s__Phenylobacterium sp013822795	80.1521	629	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297125.1	s__Phenylobacterium sp004297125	79.8121	617	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281955.1	s__Caulobacter sp000281955	79.657	541	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	79.6439	588	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745545.1	s__Caulobacter henricii_C	79.4179	562	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.38	99.38	0.95	0.95	2	-
GCF_001427665.1	s__Caulobacter sp001427665	79.2073	602	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185805.1	s__Caulobacter sp003185805	79.1835	518	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:08:04,410] [INFO] GTDB search result was written to OceanDNA-b23460/result_gtdb.tsv
[2023-03-18 07:08:04,410] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:08:04,411] [INFO] DFAST_QC result json was written to OceanDNA-b23460/dqc_result.json
[2023-03-18 07:08:04,412] [INFO] DFAST_QC completed!
[2023-03-18 07:08:04,412] [INFO] Total running time: 0h1m44s