[2023-03-15 11:09:10,872] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,872] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea56643-bd05-4786-b749-d61fba53159d/dqc_reference
[2023-03-15 11:09:12,109] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,109] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,109] [INFO] Running command: cat /var/lib/cwl/stg8d8ec663-8b7e-4cf0-bbe5-e8023b8252b9/OceanDNA-b34612.fa | prodigal -d OceanDNA-b34612/cds.fna -a OceanDNA-b34612/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:33,651] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:33,652] [INFO] Task started: HMMsearch
[2023-03-15 11:09:33,652] [INFO] Running command: hmmsearch --tblout OceanDNA-b34612/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea56643-bd05-4786-b749-d61fba53159d/dqc_reference/reference_markers.hmm OceanDNA-b34612/protein.faa > /dev/null
[2023-03-15 11:09:33,923] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:33,923] [INFO] Found 6/6 markers.
[2023-03-15 11:09:33,946] [INFO] Query marker FASTA was written to OceanDNA-b34612/markers.fasta
[2023-03-15 11:09:33,946] [INFO] Task started: Blastn
[2023-03-15 11:09:33,946] [INFO] Running command: blastn -query OceanDNA-b34612/markers.fasta -db /var/lib/cwl/stg4ea56643-bd05-4786-b749-d61fba53159d/dqc_reference/reference_markers.fasta -out OceanDNA-b34612/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:34,564] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:34,565] [INFO] Selected 17 target genomes.
[2023-03-15 11:09:34,565] [INFO] Target genome list was writen to OceanDNA-b34612/target_genomes.txt
[2023-03-15 11:09:34,575] [INFO] Task started: fastANI
[2023-03-15 11:09:34,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d8ec663-8b7e-4cf0-bbe5-e8023b8252b9/OceanDNA-b34612.fa --refList OceanDNA-b34612/target_genomes.txt --output OceanDNA-b34612/fastani_result.tsv --threads 1
[2023-03-15 11:09:46,803] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:46,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea56643-bd05-4786-b749-d61fba53159d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:46,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea56643-bd05-4786-b749-d61fba53159d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:46,812] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:46,812] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:46,813] [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
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	81.5441	811	1239	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	81.416	784	1239	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	81.3854	750	1239	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	78.5304	425	1239	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.5271	378	1239	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	78.5187	416	1239	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	78.5038	374	1239	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.4548	397	1239	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.4121	422	1239	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	78.007	285	1239	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	77.8839	283	1239	95	below_threshold
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	77.846	292	1239	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	76.9262	165	1239	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	76.903	165	1239	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:46,813] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34612/tc_result.tsv
[2023-03-15 11:09:46,813] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:46,813] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:46,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea56643-bd05-4786-b749-d61fba53159d/dqc_reference/checkm_data
[2023-03-15 11:09:46,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:46,819] [INFO] Task started: CheckM
[2023-03-15 11:09:46,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34612/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34612/checkm_input OceanDNA-b34612/checkm_result
[2023-03-15 11:10:41,270] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:41,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:41,273] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:41,273] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:41,273] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34612/markers.fasta)
[2023-03-15 11:10:41,274] [INFO] Task started: Blastn
[2023-03-15 11:10:41,274] [INFO] Running command: blastn -query OceanDNA-b34612/markers.fasta -db /var/lib/cwl/stg4ea56643-bd05-4786-b749-d61fba53159d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34612/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:42,095] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:42,095] [INFO] Selected 10 target genomes.
[2023-03-15 11:10:42,095] [INFO] Target genome list was writen to OceanDNA-b34612/target_genomes_gtdb.txt
[2023-03-15 11:10:42,103] [INFO] Task started: fastANI
[2023-03-15 11:10:42,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d8ec663-8b7e-4cf0-bbe5-e8023b8252b9/OceanDNA-b34612.fa --refList OceanDNA-b34612/target_genomes_gtdb.txt --output OceanDNA-b34612/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:50,056] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:50,062] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:50,062] [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_002364615.1	s__Arsukibacterium sp002364615	82.8207	816	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCA_002415085.1	s__Arsukibacterium sp002415085	81.7886	807	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	-
GCF_019100565.1	s__Arsukibacterium sp019100565	81.5441	811	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	81.4734	800	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	81.4168	784	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382165.1	s__Arsukibacterium perlucidum	81.3821	749	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	81.1187	758	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987765.1	s__Arsukibacterium sp000987765	79.7492	577	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:50,062] [INFO] GTDB search result was written to OceanDNA-b34612/result_gtdb.tsv
[2023-03-15 11:10:50,062] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:50,063] [INFO] DFAST_QC result json was written to OceanDNA-b34612/dqc_result.json
[2023-03-15 11:10:50,064] [INFO] DFAST_QC completed!
[2023-03-15 11:10:50,064] [INFO] Total running time: 0h1m39s