[2023-03-16 04:54:07,033] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,033] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,033] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1c88d28-7da6-49b1-9037-7610a316a438/dqc_reference
[2023-03-16 04:54:08,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,365] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,365] [INFO] Running command: cat /var/lib/cwl/stg8299f2e8-cce7-4955-bb02-a6f73ec1a311/OceanDNA-b31464.fa | prodigal -d OceanDNA-b31464/cds.fna -a OceanDNA-b31464/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:29,091] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:29,092] [INFO] Task started: HMMsearch
[2023-03-16 04:54:29,092] [INFO] Running command: hmmsearch --tblout OceanDNA-b31464/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1c88d28-7da6-49b1-9037-7610a316a438/dqc_reference/reference_markers.hmm OceanDNA-b31464/protein.faa > /dev/null
[2023-03-16 04:54:29,395] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:29,396] [INFO] Found 6/6 markers.
[2023-03-16 04:54:29,422] [INFO] Query marker FASTA was written to OceanDNA-b31464/markers.fasta
[2023-03-16 04:54:29,422] [INFO] Task started: Blastn
[2023-03-16 04:54:29,422] [INFO] Running command: blastn -query OceanDNA-b31464/markers.fasta -db /var/lib/cwl/stgd1c88d28-7da6-49b1-9037-7610a316a438/dqc_reference/reference_markers.fasta -out OceanDNA-b31464/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:30,150] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:30,151] [INFO] Selected 20 target genomes.
[2023-03-16 04:54:30,151] [INFO] Target genome list was writen to OceanDNA-b31464/target_genomes.txt
[2023-03-16 04:54:30,164] [INFO] Task started: fastANI
[2023-03-16 04:54:30,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg8299f2e8-cce7-4955-bb02-a6f73ec1a311/OceanDNA-b31464.fa --refList OceanDNA-b31464/target_genomes.txt --output OceanDNA-b31464/fastani_result.tsv --threads 1
[2023-03-16 04:54:45,610] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:45,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1c88d28-7da6-49b1-9037-7610a316a438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:45,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1c88d28-7da6-49b1-9037-7610a316a438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:45,618] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:45,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:54:45,619] [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
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	79.4804	548	1110	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	79.4596	556	1110	95	below_threshold
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	78.7029	435	1110	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	78.1559	384	1110	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	76.897	223	1110	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.183	88	1110	95	below_threshold
Sneathiella aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	76.1639	64	1110	95	below_threshold
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	76.1504	55	1110	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.4734	63	1110	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.4253	64	1110	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.2949	64	1110	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:54:45,619] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31464/tc_result.tsv
[2023-03-16 04:54:45,620] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:45,620] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:45,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1c88d28-7da6-49b1-9037-7610a316a438/dqc_reference/checkm_data
[2023-03-16 04:54:45,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:45,626] [INFO] Task started: CheckM
[2023-03-16 04:54:45,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31464/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31464/checkm_input OceanDNA-b31464/checkm_result
[2023-03-16 04:55:37,695] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:37,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:37,698] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:37,698] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:37,698] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31464/markers.fasta)
[2023-03-16 04:55:37,699] [INFO] Task started: Blastn
[2023-03-16 04:55:37,699] [INFO] Running command: blastn -query OceanDNA-b31464/markers.fasta -db /var/lib/cwl/stgd1c88d28-7da6-49b1-9037-7610a316a438/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31464/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:38,939] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:38,940] [INFO] Selected 13 target genomes.
[2023-03-16 04:55:38,940] [INFO] Target genome list was writen to OceanDNA-b31464/target_genomes_gtdb.txt
[2023-03-16 04:55:38,955] [INFO] Task started: fastANI
[2023-03-16 04:55:38,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg8299f2e8-cce7-4955-bb02-a6f73ec1a311/OceanDNA-b31464.fa --refList OceanDNA-b31464/target_genomes_gtdb.txt --output OceanDNA-b31464/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:48,308] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:48,314] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:55:48,314] [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_002694385.1	s__Sneathiella sp002694385	99.7436	1104	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	conclusive
GCF_009882935.1	s__Sneathiella chungangensis	79.4894	547	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002706985.1	s__Sneathiella sp002706985	79.3685	442	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
GCF_017313765.1	s__Sneathiella sp017313765	78.7029	435	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882915.1	s__Sneathiella litorea	78.16	383	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226265.1	s__Sneathiella sp006226265	78.1175	283	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015143595.1	s__Sneathiella sp015143595	76.1594	54	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827955.1	s__Nitrospirillum amazonense_B	75.6572	50	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	75.4253	64	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574735.1	s__SYSU-D60009 sp003574735	75.3636	54	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60009	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:48,315] [INFO] GTDB search result was written to OceanDNA-b31464/result_gtdb.tsv
[2023-03-16 04:55:48,315] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:48,316] [INFO] DFAST_QC result json was written to OceanDNA-b31464/dqc_result.json
[2023-03-16 04:55:48,316] [INFO] DFAST_QC completed!
[2023-03-16 04:55:48,316] [INFO] Total running time: 0h1m41s