[2023-03-17 00:45:47,219] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,219] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf79be4f-703b-4eb0-849f-b027e48da7d5/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stg3f514042-e891-4430-b479-62375ddb7091/OceanDNA-b7477.fa | prodigal -d OceanDNA-b7477/cds.fna -a OceanDNA-b7477/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:04,106] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:04,106] [INFO] Task started: HMMsearch
[2023-03-17 00:46:04,106] [INFO] Running command: hmmsearch --tblout OceanDNA-b7477/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf79be4f-703b-4eb0-849f-b027e48da7d5/dqc_reference/reference_markers.hmm OceanDNA-b7477/protein.faa > /dev/null
[2023-03-17 00:46:04,306] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:04,307] [INFO] Found 6/6 markers.
[2023-03-17 00:46:04,328] [INFO] Query marker FASTA was written to OceanDNA-b7477/markers.fasta
[2023-03-17 00:46:04,328] [INFO] Task started: Blastn
[2023-03-17 00:46:04,328] [INFO] Running command: blastn -query OceanDNA-b7477/markers.fasta -db /var/lib/cwl/stgcf79be4f-703b-4eb0-849f-b027e48da7d5/dqc_reference/reference_markers.fasta -out OceanDNA-b7477/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:04,888] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:04,888] [INFO] Selected 27 target genomes.
[2023-03-17 00:46:04,889] [INFO] Target genome list was writen to OceanDNA-b7477/target_genomes.txt
[2023-03-17 00:46:04,962] [INFO] Task started: fastANI
[2023-03-17 00:46:04,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f514042-e891-4430-b479-62375ddb7091/OceanDNA-b7477.fa --refList OceanDNA-b7477/target_genomes.txt --output OceanDNA-b7477/fastani_result.tsv --threads 1
[2023-03-17 00:46:20,899] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:20,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf79be4f-703b-4eb0-849f-b027e48da7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:20,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf79be4f-703b-4eb0-849f-b027e48da7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:20,908] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:20,908] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:20,908] [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
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	77.0269	137	780	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	76.9814	139	780	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	76.8201	138	780	95	below_threshold
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	76.6016	123	780	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	76.5214	117	780	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	76.5214	117	780	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	76.4704	118	780	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	75.6567	59	780	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.5704	51	780	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	75.4301	53	780	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	75.4102	54	780	95	below_threshold
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	75.4086	57	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:20,908] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7477/tc_result.tsv
[2023-03-17 00:46:20,908] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:20,908] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:20,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf79be4f-703b-4eb0-849f-b027e48da7d5/dqc_reference/checkm_data
[2023-03-17 00:46:20,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:20,914] [INFO] Task started: CheckM
[2023-03-17 00:46:20,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7477/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7477/checkm_input OceanDNA-b7477/checkm_result
[2023-03-17 00:47:03,037] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:03,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:03,040] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:03,040] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:03,040] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7477/markers.fasta)
[2023-03-17 00:47:03,041] [INFO] Task started: Blastn
[2023-03-17 00:47:03,042] [INFO] Running command: blastn -query OceanDNA-b7477/markers.fasta -db /var/lib/cwl/stgcf79be4f-703b-4eb0-849f-b027e48da7d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7477/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:03,835] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:03,836] [INFO] Selected 24 target genomes.
[2023-03-17 00:47:03,836] [INFO] Target genome list was writen to OceanDNA-b7477/target_genomes_gtdb.txt
[2023-03-17 00:47:04,074] [INFO] Task started: fastANI
[2023-03-17 00:47:04,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f514042-e891-4430-b479-62375ddb7091/OceanDNA-b7477.fa --refList OceanDNA-b7477/target_genomes_gtdb.txt --output OceanDNA-b7477/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:19,632] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:19,642] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:19,643] [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
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	77.0269	137	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	76.8201	138	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	76.7924	156	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	76.727	139	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104375.1	s__Leeuwenhoekiella aequorea	76.6016	123	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	76.5214	117	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	76.4704	118	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_000733945.1	s__Leeuwenhoekiella sp000733945	76.2308	101	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050015.1	s__Leeuwenhoekiella sp011050015	75.993	67	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	75.6975	61	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632745.1	s__Aquimarina aggregata	75.6567	59	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCF_007827465.1	s__Dokdonia sp007827465	75.6047	57	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745315.1	s__Salegentibacter sp000745315	75.5679	51	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443675.1	s__Aquimarina sp003443675	75.5358	64	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900142975.1	s__Salegentibacter salegens	75.4301	53	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016735115.1	s__Aquimarina mytili	75.4086	57	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	75.3491	57	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_007489275.1	s__Aquimarina algiphila	75.2392	57	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:19,643] [INFO] GTDB search result was written to OceanDNA-b7477/result_gtdb.tsv
[2023-03-17 00:47:19,643] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:19,645] [INFO] DFAST_QC result json was written to OceanDNA-b7477/dqc_result.json
[2023-03-17 00:47:19,645] [INFO] DFAST_QC completed!
[2023-03-17 00:47:19,645] [INFO] Total running time: 0h1m32s