[2023-03-14 12:03:55,349] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,358] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa28aca1-79bb-472d-b2f9-614533456b0e/dqc_reference
[2023-03-14 12:03:56,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,864] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,864] [INFO] Running command: cat /var/lib/cwl/stg37a8f3fd-db58-4f37-8d08-ba0b0b532c4a/OceanDNA-b39144.fa | prodigal -d OceanDNA-b39144/cds.fna -a OceanDNA-b39144/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:23,878] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:23,878] [INFO] Task started: HMMsearch
[2023-03-14 12:04:23,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b39144/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa28aca1-79bb-472d-b2f9-614533456b0e/dqc_reference/reference_markers.hmm OceanDNA-b39144/protein.faa > /dev/null
[2023-03-14 12:04:24,129] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:24,130] [INFO] Found 6/6 markers.
[2023-03-14 12:04:24,199] [INFO] Query marker FASTA was written to OceanDNA-b39144/markers.fasta
[2023-03-14 12:04:24,199] [INFO] Task started: Blastn
[2023-03-14 12:04:24,199] [INFO] Running command: blastn -query OceanDNA-b39144/markers.fasta -db /var/lib/cwl/stgfa28aca1-79bb-472d-b2f9-614533456b0e/dqc_reference/reference_markers.fasta -out OceanDNA-b39144/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:24,976] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:24,989] [INFO] Selected 13 target genomes.
[2023-03-14 12:04:24,990] [INFO] Target genome list was writen to OceanDNA-b39144/target_genomes.txt
[2023-03-14 12:04:24,998] [INFO] Task started: fastANI
[2023-03-14 12:04:24,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg37a8f3fd-db58-4f37-8d08-ba0b0b532c4a/OceanDNA-b39144.fa --refList OceanDNA-b39144/target_genomes.txt --output OceanDNA-b39144/fastani_result.tsv --threads 1
[2023-03-14 12:04:35,627] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:35,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa28aca1-79bb-472d-b2f9-614533456b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:35,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa28aca1-79bb-472d-b2f9-614533456b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:35,637] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:35,637] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:04:35,637] [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	92.8829	1144	1422	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	82.0452	881	1422	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	81.5423	742	1422	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	81.4665	736	1422	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	81.435	708	1422	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	81.3314	726	1422	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.8806	559	1422	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	79.7129	588	1422	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.6198	543	1422	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	79.5466	543	1422	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.3668	549	1422	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.9268	373	1422	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.6604	456	1422	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:35,646] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39144/tc_result.tsv
[2023-03-14 12:04:35,658] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:35,658] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:35,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa28aca1-79bb-472d-b2f9-614533456b0e/dqc_reference/checkm_data
[2023-03-14 12:04:35,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:35,689] [INFO] Task started: CheckM
[2023-03-14 12:04:35,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39144/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39144/checkm_input OceanDNA-b39144/checkm_result
[2023-03-14 12:05:41,607] [INFO] Task succeeded: CheckM
[2023-03-14 12:05:41,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:05:41,632] [INFO] ===== Completeness check finished =====
[2023-03-14 12:05:41,633] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:05:41,633] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39144/markers.fasta)
[2023-03-14 12:05:41,634] [INFO] Task started: Blastn
[2023-03-14 12:05:41,634] [INFO] Running command: blastn -query OceanDNA-b39144/markers.fasta -db /var/lib/cwl/stgfa28aca1-79bb-472d-b2f9-614533456b0e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39144/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:05:42,959] [INFO] Task succeeded: Blastn
[2023-03-14 12:05:42,975] [INFO] Selected 9 target genomes.
[2023-03-14 12:05:42,976] [INFO] Target genome list was writen to OceanDNA-b39144/target_genomes_gtdb.txt
[2023-03-14 12:05:43,029] [INFO] Task started: fastANI
[2023-03-14 12:05:43,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg37a8f3fd-db58-4f37-8d08-ba0b0b532c4a/OceanDNA-b39144.fa --refList OceanDNA-b39144/target_genomes_gtdb.txt --output OceanDNA-b39144/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:05:51,571] [INFO] Task succeeded: fastANI
[2023-03-14 12:05:51,577] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:05:51,577] [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_002726615.1	s__Marinobacter sp002726615	99.1008	861	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	conclusive
GCF_000170835.1	s__Marinobacter algicola	92.8763	1144	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000831005.1	s__Marinobacter salarius	92.0618	1219	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	-
GCF_008795955.1	s__Marinobacter sp008795955	82.0591	879	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000686085.1	s__Marinobacter sp000686085	82.0358	823	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005298175.1	s__Marinobacter sp005298175	81.9458	895	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	81.4721	735	1422	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	81.3314	726	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008795985.1	s__Marinobacter halotolerans	79.5466	543	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:05:51,584] [INFO] GTDB search result was written to OceanDNA-b39144/result_gtdb.tsv
[2023-03-14 12:05:51,595] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:05:51,603] [INFO] DFAST_QC result json was written to OceanDNA-b39144/dqc_result.json
[2023-03-14 12:05:51,603] [INFO] DFAST_QC completed!
[2023-03-14 12:05:51,603] [INFO] Total running time: 0h1m56s