[2023-03-18 02:27:59,037] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:59,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:59,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c7c3a29-3c89-4047-961d-efa71b32be7b/dqc_reference
[2023-03-18 02:28:00,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:28:00,133] [INFO] Task started: Prodigal
[2023-03-18 02:28:00,133] [INFO] Running command: cat /var/lib/cwl/stg3f2e2173-2dde-4cad-8ed8-85403db9def3/OceanDNA-b32925.fa | prodigal -d OceanDNA-b32925/cds.fna -a OceanDNA-b32925/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:16,162] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:16,162] [INFO] Task started: HMMsearch
[2023-03-18 02:28:16,162] [INFO] Running command: hmmsearch --tblout OceanDNA-b32925/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c7c3a29-3c89-4047-961d-efa71b32be7b/dqc_reference/reference_markers.hmm OceanDNA-b32925/protein.faa > /dev/null
[2023-03-18 02:28:16,351] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:16,351] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3f2e2173-2dde-4cad-8ed8-85403db9def3/OceanDNA-b32925.fa]
[2023-03-18 02:28:16,374] [INFO] Query marker FASTA was written to OceanDNA-b32925/markers.fasta
[2023-03-18 02:28:16,374] [INFO] Task started: Blastn
[2023-03-18 02:28:16,374] [INFO] Running command: blastn -query OceanDNA-b32925/markers.fasta -db /var/lib/cwl/stg8c7c3a29-3c89-4047-961d-efa71b32be7b/dqc_reference/reference_markers.fasta -out OceanDNA-b32925/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:17,008] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:17,009] [INFO] Selected 23 target genomes.
[2023-03-18 02:28:17,009] [INFO] Target genome list was writen to OceanDNA-b32925/target_genomes.txt
[2023-03-18 02:28:17,022] [INFO] Task started: fastANI
[2023-03-18 02:28:17,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f2e2173-2dde-4cad-8ed8-85403db9def3/OceanDNA-b32925.fa --refList OceanDNA-b32925/target_genomes.txt --output OceanDNA-b32925/fastani_result.tsv --threads 1
[2023-03-18 02:28:32,768] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:32,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c7c3a29-3c89-4047-961d-efa71b32be7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:32,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c7c3a29-3c89-4047-961d-efa71b32be7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:32,774] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:32,775] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:32,775] [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 pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.6933	58	821	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.6284	83	821	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.6282	64	821	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.5774	53	821	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.4839	63	821	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.3954	89	821	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.3727	71	821	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.351	70	821	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.186	59	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:32,775] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32925/tc_result.tsv
[2023-03-18 02:28:32,775] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:32,775] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:32,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c7c3a29-3c89-4047-961d-efa71b32be7b/dqc_reference/checkm_data
[2023-03-18 02:28:32,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:32,780] [INFO] Task started: CheckM
[2023-03-18 02:28:32,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32925/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32925/checkm_input OceanDNA-b32925/checkm_result
[2023-03-18 02:29:14,912] [INFO] Task succeeded: CheckM
[2023-03-18 02:29:14,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.59%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:29:14,915] [INFO] ===== Completeness check finished =====
[2023-03-18 02:29:14,915] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:29:14,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32925/markers.fasta)
[2023-03-18 02:29:14,915] [INFO] Task started: Blastn
[2023-03-18 02:29:14,915] [INFO] Running command: blastn -query OceanDNA-b32925/markers.fasta -db /var/lib/cwl/stg8c7c3a29-3c89-4047-961d-efa71b32be7b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32925/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:29:16,052] [INFO] Task succeeded: Blastn
[2023-03-18 02:29:16,053] [INFO] Selected 19 target genomes.
[2023-03-18 02:29:16,053] [INFO] Target genome list was writen to OceanDNA-b32925/target_genomes_gtdb.txt
[2023-03-18 02:29:16,070] [INFO] Task started: fastANI
[2023-03-18 02:29:16,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f2e2173-2dde-4cad-8ed8-85403db9def3/OceanDNA-b32925.fa --refList OceanDNA-b32925/target_genomes_gtdb.txt --output OceanDNA-b32925/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:28,870] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:28,878] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:29:28,878] [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_018666805.1	s__PTKB01 sp018666805	83.2754	626	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_002937555.1	s__PTKB01 sp002937555	79.7841	369	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691045.1	s__SHWC01 sp009691045	76.1018	76	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__SHWC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.8128	53	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.6933	58	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	75.5774	53	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCA_902826565.1	s__CADEFF01 sp902826565	75.5728	76	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	75.5159	82	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824785.1	s__Mesorhizobium plurifarium	75.4794	60	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCF_003952465.1	s__Mesorhizobium sp003952465	75.4601	58	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCA_009377375.1	s__WHUE01 sp009377375	75.3402	67	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	75.2639	65	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791585.1	s__Mesorhizobium sp004791585	75.0696	56	821	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:28,878] [INFO] GTDB search result was written to OceanDNA-b32925/result_gtdb.tsv
[2023-03-18 02:29:28,878] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:28,879] [INFO] DFAST_QC result json was written to OceanDNA-b32925/dqc_result.json
[2023-03-18 02:29:28,879] [INFO] DFAST_QC completed!
[2023-03-18 02:29:28,880] [INFO] Total running time: 0h1m30s