[2023-03-16 21:45:15,247] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,247] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,248] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7788b7c-cd4c-413f-9a04-b4d9de111eaf/dqc_reference
[2023-03-16 21:45:16,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,366] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,366] [INFO] Running command: cat /var/lib/cwl/stgcfe4c8e5-388c-4a48-996f-f9235406a5ea/OceanDNA-b23463.fa | prodigal -d OceanDNA-b23463/cds.fna -a OceanDNA-b23463/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:24,520] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:24,521] [INFO] Task started: HMMsearch
[2023-03-16 21:45:24,521] [INFO] Running command: hmmsearch --tblout OceanDNA-b23463/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7788b7c-cd4c-413f-9a04-b4d9de111eaf/dqc_reference/reference_markers.hmm OceanDNA-b23463/protein.faa > /dev/null
[2023-03-16 21:45:24,717] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:24,717] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcfe4c8e5-388c-4a48-996f-f9235406a5ea/OceanDNA-b23463.fa]
[2023-03-16 21:45:24,735] [INFO] Query marker FASTA was written to OceanDNA-b23463/markers.fasta
[2023-03-16 21:45:24,736] [INFO] Task started: Blastn
[2023-03-16 21:45:24,736] [INFO] Running command: blastn -query OceanDNA-b23463/markers.fasta -db /var/lib/cwl/stgd7788b7c-cd4c-413f-9a04-b4d9de111eaf/dqc_reference/reference_markers.fasta -out OceanDNA-b23463/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:25,396] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:25,396] [INFO] Selected 13 target genomes.
[2023-03-16 21:45:25,397] [INFO] Target genome list was writen to OceanDNA-b23463/target_genomes.txt
[2023-03-16 21:45:25,405] [INFO] Task started: fastANI
[2023-03-16 21:45:25,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe4c8e5-388c-4a48-996f-f9235406a5ea/OceanDNA-b23463.fa --refList OceanDNA-b23463/target_genomes.txt --output OceanDNA-b23463/fastani_result.tsv --threads 1
[2023-03-16 21:45:34,580] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:34,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7788b7c-cd4c-413f-9a04-b4d9de111eaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:34,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7788b7c-cd4c-413f-9a04-b4d9de111eaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:34,589] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:34,589] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:34,590] [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	80.2917	234	362	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	80.0153	240	362	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	79.9365	204	362	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.6271	206	362	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.2715	181	362	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.0462	171	362	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	79.0217	203	362	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	78.8037	179	362	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	78.7779	159	362	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	78.7643	177	362	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.5548	179	362	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.2039	60	362	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.2896	64	362	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:34,590] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23463/tc_result.tsv
[2023-03-16 21:45:34,590] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:34,590] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:34,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7788b7c-cd4c-413f-9a04-b4d9de111eaf/dqc_reference/checkm_data
[2023-03-16 21:45:34,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:34,595] [INFO] Task started: CheckM
[2023-03-16 21:45:34,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23463/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23463/checkm_input OceanDNA-b23463/checkm_result
[2023-03-16 21:46:00,099] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:00,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:00,101] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:00,101] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:00,102] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23463/markers.fasta)
[2023-03-16 21:46:00,102] [INFO] Task started: Blastn
[2023-03-16 21:46:00,102] [INFO] Running command: blastn -query OceanDNA-b23463/markers.fasta -db /var/lib/cwl/stgd7788b7c-cd4c-413f-9a04-b4d9de111eaf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23463/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:01,180] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:01,182] [INFO] Selected 9 target genomes.
[2023-03-16 21:46:01,182] [INFO] Target genome list was writen to OceanDNA-b23463/target_genomes_gtdb.txt
[2023-03-16 21:46:01,193] [INFO] Task started: fastANI
[2023-03-16 21:46:01,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe4c8e5-388c-4a48-996f-f9235406a5ea/OceanDNA-b23463.fa --refList OceanDNA-b23463/target_genomes_gtdb.txt --output OceanDNA-b23463/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:07,089] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:07,095] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:07,095] [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	91.3876	346	362	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	87.7378	285	362	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	83.5222	292	362	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	80.3465	226	362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCF_000017265.1	s__Phenylobacterium zucineum	79.6271	206	362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_013822795.1	s__Phenylobacterium sp013822795	79.6067	194	362	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	79.496	208	362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_003254475.1	s__Phenylobacterium soli	79.2715	181	362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	78.498	191	362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:07,095] [INFO] GTDB search result was written to OceanDNA-b23463/result_gtdb.tsv
[2023-03-16 21:46:07,095] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:07,096] [INFO] DFAST_QC result json was written to OceanDNA-b23463/dqc_result.json
[2023-03-16 21:46:07,097] [INFO] DFAST_QC completed!
[2023-03-16 21:46:07,097] [INFO] Total running time: 0h0m52s