[2023-03-16 22:05:57,079] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:05:57,079] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:05:57,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg22263ed8-629e-4b43-8a22-bce5e7afcac1/dqc_reference
[2023-03-16 22:05:58,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:05:58,248] [INFO] Task started: Prodigal
[2023-03-16 22:05:58,248] [INFO] Running command: cat /var/lib/cwl/stg9810027f-1aa9-421e-bab6-723ee72bbdd8/OceanDNA-b36675.fa | prodigal -d OceanDNA-b36675/cds.fna -a OceanDNA-b36675/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:06:18,439] [INFO] Task succeeded: Prodigal
[2023-03-16 22:06:18,439] [INFO] Task started: HMMsearch
[2023-03-16 22:06:18,439] [INFO] Running command: hmmsearch --tblout OceanDNA-b36675/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22263ed8-629e-4b43-8a22-bce5e7afcac1/dqc_reference/reference_markers.hmm OceanDNA-b36675/protein.faa > /dev/null
[2023-03-16 22:06:18,641] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:06:18,642] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9810027f-1aa9-421e-bab6-723ee72bbdd8/OceanDNA-b36675.fa]
[2023-03-16 22:06:18,661] [INFO] Query marker FASTA was written to OceanDNA-b36675/markers.fasta
[2023-03-16 22:06:18,661] [INFO] Task started: Blastn
[2023-03-16 22:06:18,661] [INFO] Running command: blastn -query OceanDNA-b36675/markers.fasta -db /var/lib/cwl/stg22263ed8-629e-4b43-8a22-bce5e7afcac1/dqc_reference/reference_markers.fasta -out OceanDNA-b36675/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:19,274] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:19,275] [INFO] Selected 19 target genomes.
[2023-03-16 22:06:19,275] [INFO] Target genome list was writen to OceanDNA-b36675/target_genomes.txt
[2023-03-16 22:06:19,286] [INFO] Task started: fastANI
[2023-03-16 22:06:19,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg9810027f-1aa9-421e-bab6-723ee72bbdd8/OceanDNA-b36675.fa --refList OceanDNA-b36675/target_genomes.txt --output OceanDNA-b36675/fastani_result.tsv --threads 1
[2023-03-16 22:06:32,218] [INFO] Task succeeded: fastANI
[2023-03-16 22:06:32,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22263ed8-629e-4b43-8a22-bce5e7afcac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:06:32,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22263ed8-629e-4b43-8a22-bce5e7afcac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:06:32,225] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:06:32,225] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 22:06:32,225] [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
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	79.5229	477	1119	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	78.2708	303	1119	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	76.6905	114	1119	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	76.5033	57	1119	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	76.2356	60	1119	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	76.2228	59	1119	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.1936	59	1119	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.099	78	1119	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 22:06:32,225] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36675/tc_result.tsv
[2023-03-16 22:06:32,225] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:06:32,225] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:06:32,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22263ed8-629e-4b43-8a22-bce5e7afcac1/dqc_reference/checkm_data
[2023-03-16 22:06:32,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:06:32,230] [INFO] Task started: CheckM
[2023-03-16 22:06:32,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36675/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36675/checkm_input OceanDNA-b36675/checkm_result
[2023-03-16 22:07:22,794] [INFO] Task succeeded: CheckM
[2023-03-16 22:07:22,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:07:22,796] [INFO] ===== Completeness check finished =====
[2023-03-16 22:07:22,797] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:07:22,797] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36675/markers.fasta)
[2023-03-16 22:07:22,798] [INFO] Task started: Blastn
[2023-03-16 22:07:22,798] [INFO] Running command: blastn -query OceanDNA-b36675/markers.fasta -db /var/lib/cwl/stg22263ed8-629e-4b43-8a22-bce5e7afcac1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36675/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:07:23,722] [INFO] Task succeeded: Blastn
[2023-03-16 22:07:23,723] [INFO] Selected 13 target genomes.
[2023-03-16 22:07:23,723] [INFO] Target genome list was writen to OceanDNA-b36675/target_genomes_gtdb.txt
[2023-03-16 22:07:23,968] [INFO] Task started: fastANI
[2023-03-16 22:07:23,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg9810027f-1aa9-421e-bab6-723ee72bbdd8/OceanDNA-b36675.fa --refList OceanDNA-b36675/target_genomes_gtdb.txt --output OceanDNA-b36675/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:07:32,956] [INFO] Task succeeded: fastANI
[2023-03-16 22:07:32,961] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 22:07:32,962] [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_000832015.1	s__Gilvimarinus agarilyticus	87.8666	878	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187555.1	s__Gilvimarinus polysaccharolyticus	79.5176	478	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377745.1	s__Gilvimarinus chinensis	78.2581	304	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	76.7085	113	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423345.1	s__Marinimicrobium agarilyticum	76.5282	109	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	76.448	106	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	76.2356	60	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	76.0643	77	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_000953825.1	s__Cellvibrio sp000953825	75.9971	93	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 22:07:32,962] [INFO] GTDB search result was written to OceanDNA-b36675/result_gtdb.tsv
[2023-03-16 22:07:32,962] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:07:32,963] [INFO] DFAST_QC result json was written to OceanDNA-b36675/dqc_result.json
[2023-03-16 22:07:32,963] [INFO] DFAST_QC completed!
[2023-03-16 22:07:32,963] [INFO] Total running time: 0h1m36s