[2023-03-16 04:24:46,336] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgcaa037df-3bc4-49ef-a9f8-fa1fa75089e4/dqc_reference
[2023-03-16 04:24:48,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,114] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,114] [INFO] Running command: cat /var/lib/cwl/stgf4ab7256-8896-4aed-bc91-816ab4510eae/OceanDNA-b29873.fa | prodigal -d OceanDNA-b29873/cds.fna -a OceanDNA-b29873/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:01,076] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:01,076] [INFO] Task started: HMMsearch
[2023-03-16 04:25:01,076] [INFO] Running command: hmmsearch --tblout OceanDNA-b29873/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcaa037df-3bc4-49ef-a9f8-fa1fa75089e4/dqc_reference/reference_markers.hmm OceanDNA-b29873/protein.faa > /dev/null
[2023-03-16 04:25:01,302] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:01,303] [INFO] Found 6/6 markers.
[2023-03-16 04:25:01,320] [INFO] Query marker FASTA was written to OceanDNA-b29873/markers.fasta
[2023-03-16 04:25:01,320] [INFO] Task started: Blastn
[2023-03-16 04:25:01,320] [INFO] Running command: blastn -query OceanDNA-b29873/markers.fasta -db /var/lib/cwl/stgcaa037df-3bc4-49ef-a9f8-fa1fa75089e4/dqc_reference/reference_markers.fasta -out OceanDNA-b29873/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:01,898] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:01,898] [INFO] Selected 29 target genomes.
[2023-03-16 04:25:01,899] [INFO] Target genome list was writen to OceanDNA-b29873/target_genomes.txt
[2023-03-16 04:25:01,911] [INFO] Task started: fastANI
[2023-03-16 04:25:01,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ab7256-8896-4aed-bc91-816ab4510eae/OceanDNA-b29873.fa --refList OceanDNA-b29873/target_genomes.txt --output OceanDNA-b29873/fastani_result.tsv --threads 1
[2023-03-16 04:25:20,356] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:20,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcaa037df-3bc4-49ef-a9f8-fa1fa75089e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:20,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcaa037df-3bc4-49ef-a9f8-fa1fa75089e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:20,363] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:20,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:25:20,363] [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
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	87.36	612	650	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.7835	65	650	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	75.7732	58	650	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	75.771	57	650	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	75.7048	55	650	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	75.6824	62	650	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	75.63	56	650	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	75.6099	55	650	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:25:20,364] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29873/tc_result.tsv
[2023-03-16 04:25:20,364] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:20,364] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:20,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcaa037df-3bc4-49ef-a9f8-fa1fa75089e4/dqc_reference/checkm_data
[2023-03-16 04:25:20,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:20,371] [INFO] Task started: CheckM
[2023-03-16 04:25:20,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29873/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29873/checkm_input OceanDNA-b29873/checkm_result
[2023-03-16 04:25:56,753] [INFO] Task succeeded: CheckM
[2023-03-16 04:25:56,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:25:56,755] [INFO] ===== Completeness check finished =====
[2023-03-16 04:25:56,755] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:25:56,755] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29873/markers.fasta)
[2023-03-16 04:25:56,756] [INFO] Task started: Blastn
[2023-03-16 04:25:56,757] [INFO] Running command: blastn -query OceanDNA-b29873/markers.fasta -db /var/lib/cwl/stgcaa037df-3bc4-49ef-a9f8-fa1fa75089e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29873/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:57,558] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:57,558] [INFO] Selected 11 target genomes.
[2023-03-16 04:25:57,559] [INFO] Target genome list was writen to OceanDNA-b29873/target_genomes_gtdb.txt
[2023-03-16 04:25:57,570] [INFO] Task started: fastANI
[2023-03-16 04:25:57,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ab7256-8896-4aed-bc91-816ab4510eae/OceanDNA-b29873.fa --refList OceanDNA-b29873/target_genomes_gtdb.txt --output OceanDNA-b29873/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:26:04,207] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:04,213] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:26:04,213] [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_002683685.1	s__Planktomarina sp002683685	95.2496	458	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	95.59	95.45	0.70	0.67	6	conclusive
GCF_000738435.1	s__Planktomarina temperata	87.36	612	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	-
GCA_905181815.1	s__Planktomarina sp905181815	87.1816	569	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780825.1	s__Planktomarina sp016780825	86.5331	555	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182455.1	s__Planktomarina sp905182455	77.569	233	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981705.1	s__Planktomarina sp000981705	76.8318	133	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	-
GCF_900115165.1	s__Roseovarius lutimaris	75.9287	54	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	75.7048	55	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	75.5292	50	650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-16 04:26:04,213] [INFO] GTDB search result was written to OceanDNA-b29873/result_gtdb.tsv
[2023-03-16 04:26:04,213] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:26:04,215] [INFO] DFAST_QC result json was written to OceanDNA-b29873/dqc_result.json
[2023-03-16 04:26:04,215] [INFO] DFAST_QC completed!
[2023-03-16 04:26:04,215] [INFO] Total running time: 0h1m18s