[2023-03-18 09:15:00,470] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,470] [INFO] DQC Reference Directory: /var/lib/cwl/stga8f76f4b-6c1a-4668-83d2-1e3ea91db4f9/dqc_reference
[2023-03-18 09:15:02,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,030] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,030] [INFO] Running command: cat /var/lib/cwl/stg8e18e05c-ffb8-4da4-90c5-7fb585b0ecf8/OceanDNA-b39170.fa | prodigal -d OceanDNA-b39170/cds.fna -a OceanDNA-b39170/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:29,517] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:29,517] [INFO] Task started: HMMsearch
[2023-03-18 09:15:29,517] [INFO] Running command: hmmsearch --tblout OceanDNA-b39170/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8f76f4b-6c1a-4668-83d2-1e3ea91db4f9/dqc_reference/reference_markers.hmm OceanDNA-b39170/protein.faa > /dev/null
[2023-03-18 09:15:29,753] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:29,754] [INFO] Found 6/6 markers.
[2023-03-18 09:15:29,789] [INFO] Query marker FASTA was written to OceanDNA-b39170/markers.fasta
[2023-03-18 09:15:29,790] [INFO] Task started: Blastn
[2023-03-18 09:15:29,790] [INFO] Running command: blastn -query OceanDNA-b39170/markers.fasta -db /var/lib/cwl/stga8f76f4b-6c1a-4668-83d2-1e3ea91db4f9/dqc_reference/reference_markers.fasta -out OceanDNA-b39170/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:30,487] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:30,498] [INFO] Selected 33 target genomes.
[2023-03-18 09:15:30,498] [INFO] Target genome list was writen to OceanDNA-b39170/target_genomes.txt
[2023-03-18 09:15:30,519] [INFO] Task started: fastANI
[2023-03-18 09:15:30,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e18e05c-ffb8-4da4-90c5-7fb585b0ecf8/OceanDNA-b39170.fa --refList OceanDNA-b39170/target_genomes.txt --output OceanDNA-b39170/fastani_result.tsv --threads 1
[2023-03-18 09:15:50,903] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:50,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8f76f4b-6c1a-4668-83d2-1e3ea91db4f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:50,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8f76f4b-6c1a-4668-83d2-1e3ea91db4f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:50,911] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:15:50,911] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:15:50,912] [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
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	76.3181	54	1463	95	below_threshold
Marinobacter confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	76.277	54	1463	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.0444	54	1463	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	76.0342	64	1463	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.028	51	1463	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	75.8518	53	1463	95	below_threshold
Marinobacter mobilis	strain=CGMCC 1.7059	GCA_900106945.1	488533	488533	type	True	75.7948	59	1463	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	75.788	68	1463	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	75.601	50	1463	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	75.5854	52	1463	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:15:50,912] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39170/tc_result.tsv
[2023-03-18 09:15:50,912] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:50,912] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:50,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8f76f4b-6c1a-4668-83d2-1e3ea91db4f9/dqc_reference/checkm_data
[2023-03-18 09:15:50,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:50,919] [INFO] Task started: CheckM
[2023-03-18 09:15:50,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39170/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39170/checkm_input OceanDNA-b39170/checkm_result
[2023-03-18 09:16:58,110] [INFO] Task succeeded: CheckM
[2023-03-18 09:16:58,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:16:58,117] [INFO] ===== Completeness check finished =====
[2023-03-18 09:16:58,117] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:16:58,117] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39170/markers.fasta)
[2023-03-18 09:16:58,118] [INFO] Task started: Blastn
[2023-03-18 09:16:58,118] [INFO] Running command: blastn -query OceanDNA-b39170/markers.fasta -db /var/lib/cwl/stga8f76f4b-6c1a-4668-83d2-1e3ea91db4f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39170/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:16:59,308] [INFO] Task succeeded: Blastn
[2023-03-18 09:16:59,310] [INFO] Selected 29 target genomes.
[2023-03-18 09:16:59,310] [INFO] Target genome list was writen to OceanDNA-b39170/target_genomes_gtdb.txt
[2023-03-18 09:16:59,338] [INFO] Task started: fastANI
[2023-03-18 09:16:59,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e18e05c-ffb8-4da4-90c5-7fb585b0ecf8/OceanDNA-b39170.fa --refList OceanDNA-b39170/target_genomes_gtdb.txt --output OceanDNA-b39170/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:17:17,930] [INFO] Task succeeded: fastANI
[2023-03-18 09:17:17,938] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:17:17,938] [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_002354735.1	s__UBA2679 sp002354735	99.9954	1445	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__UBA2679	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000686085.1	s__Marinobacter sp000686085	76.3633	60	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004785685.1	s__Marinobacter confluentis	76.2588	56	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002260525.1	s__Hahella sp002260525	76.1584	51	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Hahella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	76.0342	64	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_900115285.1	s__Marinobacter daqiaonensis	75.8367	51	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002744735.1	s__Marinobacter guineae	75.8037	69	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003441595.1	s__Marinobacter sp003441595	75.7141	62	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807415.1	s__Pseudomonas sp002079985	75.5339	76	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	97.48	95.53	0.92	0.91	9	-
GCF_014852585.1	s__Pseudomonas sp014852585	75.4664	85	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931465.1	s__Pseudomonas_E sp000931465	75.3935	54	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:17:17,939] [INFO] GTDB search result was written to OceanDNA-b39170/result_gtdb.tsv
[2023-03-18 09:17:17,940] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:17:17,941] [INFO] DFAST_QC result json was written to OceanDNA-b39170/dqc_result.json
[2023-03-18 09:17:17,942] [INFO] DFAST_QC completed!
[2023-03-18 09:17:17,942] [INFO] Total running time: 0h2m17s