[2023-03-15 08:55:06,629] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,629] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8c0a2ea-973a-4ca6-893e-3d2b2f968c44/dqc_reference
[2023-03-15 08:55:08,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,348] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,348] [INFO] Running command: cat /var/lib/cwl/stga4f735b8-0117-4010-b9e7-582b04a3aad1/OceanDNA-b38518.fa | prodigal -d OceanDNA-b38518/cds.fna -a OceanDNA-b38518/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:26,834] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:26,834] [INFO] Task started: HMMsearch
[2023-03-15 08:55:26,834] [INFO] Running command: hmmsearch --tblout OceanDNA-b38518/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8c0a2ea-973a-4ca6-893e-3d2b2f968c44/dqc_reference/reference_markers.hmm OceanDNA-b38518/protein.faa > /dev/null
[2023-03-15 08:55:27,068] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:27,069] [INFO] Found 6/6 markers.
[2023-03-15 08:55:27,087] [INFO] Query marker FASTA was written to OceanDNA-b38518/markers.fasta
[2023-03-15 08:55:27,087] [INFO] Task started: Blastn
[2023-03-15 08:55:27,088] [INFO] Running command: blastn -query OceanDNA-b38518/markers.fasta -db /var/lib/cwl/stgf8c0a2ea-973a-4ca6-893e-3d2b2f968c44/dqc_reference/reference_markers.fasta -out OceanDNA-b38518/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:27,711] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:27,712] [INFO] Selected 29 target genomes.
[2023-03-15 08:55:27,712] [INFO] Target genome list was writen to OceanDNA-b38518/target_genomes.txt
[2023-03-15 08:55:27,722] [INFO] Task started: fastANI
[2023-03-15 08:55:27,723] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f735b8-0117-4010-b9e7-582b04a3aad1/OceanDNA-b38518.fa --refList OceanDNA-b38518/target_genomes.txt --output OceanDNA-b38518/fastani_result.tsv --threads 1
[2023-03-15 08:55:42,376] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:42,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8c0a2ea-973a-4ca6-893e-3d2b2f968c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:42,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8c0a2ea-973a-4ca6-893e-3d2b2f968c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:42,385] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:42,385] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:42,385] [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
Aquirhabdus parva	strain=HYN0046	GCA_003351745.1	2283318	2283318	type	True	77.4038	91	962	95	below_threshold
Alkanindiges hydrocarboniclasticus	strain=H1	GCA_001982605.1	1907941	1907941	type	True	76.9887	91	962	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	76.6871	66	962	95	below_threshold
Alkanindiges illinoisensis	strain=DSM 15370	GCA_000619845.1	197183	197183	type	True	76.6334	109	962	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	76.5666	65	962	95	below_threshold
Acinetobacter seohaensis	strain=DSM 16313	GCA_018403785.1	281376	281376	type	True	76.4179	51	962	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	76.3104	50	962	95	below_threshold
Acinetobacter towneri	strain=CIP 107472	GCA_000368785.1	202956	202956	type	True	76.2607	50	962	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	76.2071	58	962	95	below_threshold
Acinetobacter towneri	strain=DSM 14962	GCA_000688495.1	202956	202956	type	True	76.2025	50	962	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	75.9127	54	962	95	below_threshold
Acinetobacter soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	75.8304	58	962	95	below_threshold
Acinetobacter populi	strain=PBJ7	GCA_002174125.1	1582270	1582270	type	True	75.6968	51	962	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:42,386] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38518/tc_result.tsv
[2023-03-15 08:55:42,386] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:42,386] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:42,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8c0a2ea-973a-4ca6-893e-3d2b2f968c44/dqc_reference/checkm_data
[2023-03-15 08:55:42,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:42,394] [INFO] Task started: CheckM
[2023-03-15 08:55:42,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38518/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38518/checkm_input OceanDNA-b38518/checkm_result
[2023-03-15 08:56:30,716] [INFO] Task succeeded: CheckM
[2023-03-15 08:56:30,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:56:30,719] [INFO] ===== Completeness check finished =====
[2023-03-15 08:56:30,719] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:56:30,719] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38518/markers.fasta)
[2023-03-15 08:56:30,719] [INFO] Task started: Blastn
[2023-03-15 08:56:30,719] [INFO] Running command: blastn -query OceanDNA-b38518/markers.fasta -db /var/lib/cwl/stgf8c0a2ea-973a-4ca6-893e-3d2b2f968c44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38518/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:31,775] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:31,776] [INFO] Selected 26 target genomes.
[2023-03-15 08:56:31,776] [INFO] Target genome list was writen to OceanDNA-b38518/target_genomes_gtdb.txt
[2023-03-15 08:56:31,794] [INFO] Task started: fastANI
[2023-03-15 08:56:31,794] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f735b8-0117-4010-b9e7-582b04a3aad1/OceanDNA-b38518.fa --refList OceanDNA-b38518/target_genomes_gtdb.txt --output OceanDNA-b38518/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:44,720] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:44,730] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:56:44,730] [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_003351745.1	s__Aquirhabdus parva	77.4353	90	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Aquirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982605.1	s__Alkanindiges hydrocarboniclasticus	76.9612	92	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004377485.1	s__Alkanindiges illinoisensis_A	76.6969	107	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000488255.1	s__Acinetobacter indicus	76.6871	66	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.50	96.50	0.90	0.82	131	-
GCF_000619845.1	s__Alkanindiges illinoisensis	76.6334	109	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331155.1	s__Acinetobacter terrestris	76.547	50	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.13	95.48	0.90	0.88	5	-
GCA_004173455.1	s__Alkanindiges sp004173455	76.528	127	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008993995.1	s__Acinetobacter brisouii_A	76.4337	51	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.99	97.99	0.89	0.89	2	-
GCF_012371325.1	s__Acinetobacter sp012371325	76.3643	55	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.91	97.28	0.89	0.84	6	-
GCF_014635545.1	s__Acinetobacter courvalinii	76.3478	50	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	-
GCF_000368785.1	s__Acinetobacter towneri	76.2607	50	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.88	97.09	0.88	0.84	48	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	76.2071	58	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_001696615.3	s__Acinetobacter sp001696615	76.1951	58	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003261585.1	s__Acinetobacter sp003261585	76.1938	55	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378805.1	s__Aquirhabdus sp014378805	76.0656	75	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Aquirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002174125.1	s__Acinetobacter populi	75.6968	51	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002018365.1	s__Acinetobacter sp002018365	75.5975	52	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:44,730] [INFO] GTDB search result was written to OceanDNA-b38518/result_gtdb.tsv
[2023-03-15 08:56:44,730] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:44,732] [INFO] DFAST_QC result json was written to OceanDNA-b38518/dqc_result.json
[2023-03-15 08:56:44,732] [INFO] DFAST_QC completed!
[2023-03-15 08:56:44,732] [INFO] Total running time: 0h1m38s