[2023-03-16 04:05:20,068] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,068] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg9655e45d-50fa-4da0-8b70-58f6a5eb39d9/dqc_reference
[2023-03-16 04:05:21,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:21,132] [INFO] Task started: Prodigal
[2023-03-16 04:05:21,133] [INFO] Running command: cat /var/lib/cwl/stg73d5976c-d884-449d-92fb-e17e28a2ef2f/OceanDNA-b39096.fa | prodigal -d OceanDNA-b39096/cds.fna -a OceanDNA-b39096/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:46,732] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:46,732] [INFO] Task started: HMMsearch
[2023-03-16 04:05:46,733] [INFO] Running command: hmmsearch --tblout OceanDNA-b39096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9655e45d-50fa-4da0-8b70-58f6a5eb39d9/dqc_reference/reference_markers.hmm OceanDNA-b39096/protein.faa > /dev/null
[2023-03-16 04:05:47,064] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:47,065] [INFO] Found 6/6 markers.
[2023-03-16 04:05:47,091] [INFO] Query marker FASTA was written to OceanDNA-b39096/markers.fasta
[2023-03-16 04:05:47,091] [INFO] Task started: Blastn
[2023-03-16 04:05:47,091] [INFO] Running command: blastn -query OceanDNA-b39096/markers.fasta -db /var/lib/cwl/stg9655e45d-50fa-4da0-8b70-58f6a5eb39d9/dqc_reference/reference_markers.fasta -out OceanDNA-b39096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:50,992] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:50,992] [INFO] Selected 14 target genomes.
[2023-03-16 04:05:50,993] [INFO] Target genome list was writen to OceanDNA-b39096/target_genomes.txt
[2023-03-16 04:05:51,000] [INFO] Task started: fastANI
[2023-03-16 04:05:51,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d5976c-d884-449d-92fb-e17e28a2ef2f/OceanDNA-b39096.fa --refList OceanDNA-b39096/target_genomes.txt --output OceanDNA-b39096/fastani_result.tsv --threads 1
[2023-03-16 04:06:02,303] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:02,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9655e45d-50fa-4da0-8b70-58f6a5eb39d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:02,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9655e45d-50fa-4da0-8b70-58f6a5eb39d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:02,311] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:02,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:06:02,312] [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 algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	92.4806	1135	1365	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	82.1871	883	1365	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	81.8665	730	1365	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	81.7237	725	1365	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	81.542	722	1365	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	81.5149	718	1365	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	79.8443	562	1365	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.8171	556	1365	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.7242	537	1365	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	79.6831	585	1365	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.5278	530	1365	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	78.3043	303	1365	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.4977	104	1365	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:06:02,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39096/tc_result.tsv
[2023-03-16 04:06:02,312] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:02,312] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:02,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9655e45d-50fa-4da0-8b70-58f6a5eb39d9/dqc_reference/checkm_data
[2023-03-16 04:06:02,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:02,318] [INFO] Task started: CheckM
[2023-03-16 04:06:02,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39096/checkm_input OceanDNA-b39096/checkm_result
[2023-03-16 04:07:05,319] [INFO] Task succeeded: CheckM
[2023-03-16 04:07:05,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:07:05,322] [INFO] ===== Completeness check finished =====
[2023-03-16 04:07:05,322] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:07:05,322] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39096/markers.fasta)
[2023-03-16 04:07:05,323] [INFO] Task started: Blastn
[2023-03-16 04:07:05,323] [INFO] Running command: blastn -query OceanDNA-b39096/markers.fasta -db /var/lib/cwl/stg9655e45d-50fa-4da0-8b70-58f6a5eb39d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:07:06,597] [INFO] Task succeeded: Blastn
[2023-03-16 04:07:06,598] [INFO] Selected 8 target genomes.
[2023-03-16 04:07:06,598] [INFO] Target genome list was writen to OceanDNA-b39096/target_genomes_gtdb.txt
[2023-03-16 04:07:06,604] [INFO] Task started: fastANI
[2023-03-16 04:07:06,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d5976c-d884-449d-92fb-e17e28a2ef2f/OceanDNA-b39096.fa --refList OceanDNA-b39096/target_genomes_gtdb.txt --output OceanDNA-b39096/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:14,227] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:14,233] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:07:14,233] [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_000831005.1	s__Marinobacter salarius	97.5029	1263	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	conclusive
GCF_000170835.1	s__Marinobacter algicola	92.4944	1134	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726615.1	s__Marinobacter sp002726615	92.3724	805	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	-
GCF_005298175.1	s__Marinobacter sp005298175	82.462	844	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686085.1	s__Marinobacter sp000686085	82.2334	818	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008795955.1	s__Marinobacter sp008795955	82.1836	884	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004792665.1	s__Marinobacter orientalis	81.7237	725	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003344045.1	s__Marinobacter vulgaris	81.5055	719	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:14,233] [INFO] GTDB search result was written to OceanDNA-b39096/result_gtdb.tsv
[2023-03-16 04:07:14,233] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:14,235] [INFO] DFAST_QC result json was written to OceanDNA-b39096/dqc_result.json
[2023-03-16 04:07:14,235] [INFO] DFAST_QC completed!
[2023-03-16 04:07:14,235] [INFO] Total running time: 0h1m54s