[2023-03-19 01:38:53,904] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgb787a2c7-c339-47b2-86de-f42496974711/dqc_reference
[2023-03-19 01:38:55,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:55,004] [INFO] Task started: Prodigal
[2023-03-19 01:38:55,004] [INFO] Running command: cat /var/lib/cwl/stg61ff4f13-3db6-4c91-998b-1bc712c7df3e/OceanDNA-b6503.fa | prodigal -d OceanDNA-b6503/cds.fna -a OceanDNA-b6503/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:39:07,257] [INFO] Task succeeded: Prodigal
[2023-03-19 01:39:07,257] [INFO] Task started: HMMsearch
[2023-03-19 01:39:07,257] [INFO] Running command: hmmsearch --tblout OceanDNA-b6503/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb787a2c7-c339-47b2-86de-f42496974711/dqc_reference/reference_markers.hmm OceanDNA-b6503/protein.faa > /dev/null
[2023-03-19 01:39:07,435] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:39:07,435] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg61ff4f13-3db6-4c91-998b-1bc712c7df3e/OceanDNA-b6503.fa]
[2023-03-19 01:39:07,471] [INFO] Query marker FASTA was written to OceanDNA-b6503/markers.fasta
[2023-03-19 01:39:07,471] [INFO] Task started: Blastn
[2023-03-19 01:39:07,471] [INFO] Running command: blastn -query OceanDNA-b6503/markers.fasta -db /var/lib/cwl/stgb787a2c7-c339-47b2-86de-f42496974711/dqc_reference/reference_markers.fasta -out OceanDNA-b6503/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:08,027] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:08,031] [INFO] Selected 17 target genomes.
[2023-03-19 01:39:08,032] [INFO] Target genome list was writen to OceanDNA-b6503/target_genomes.txt
[2023-03-19 01:39:08,043] [INFO] Task started: fastANI
[2023-03-19 01:39:08,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ff4f13-3db6-4c91-998b-1bc712c7df3e/OceanDNA-b6503.fa --refList OceanDNA-b6503/target_genomes.txt --output OceanDNA-b6503/fastani_result.tsv --threads 1
[2023-03-19 01:39:20,169] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:20,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb787a2c7-c339-47b2-86de-f42496974711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:20,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb787a2c7-c339-47b2-86de-f42496974711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:20,177] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:20,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:39:20,177] [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
Aquimarina brevivitae	strain=DSM 17196	GCA_004216895.1	323412	323412	type	True	78.2664	192	509	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	77.2311	103	509	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	77.2262	114	509	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	77.2253	106	509	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	77.2202	102	509	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	77.1817	88	509	95	below_threshold
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	77.0846	99	509	95	below_threshold
Aquimarina pacifica	strain=SW150	GCA_000520955.1	1296415	1296415	type	True	76.9438	84	509	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	76.9211	117	509	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.9135	108	509	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	76.7439	106	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:39:20,181] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6503/tc_result.tsv
[2023-03-19 01:39:20,189] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:20,190] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:20,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb787a2c7-c339-47b2-86de-f42496974711/dqc_reference/checkm_data
[2023-03-19 01:39:20,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:20,207] [INFO] Task started: CheckM
[2023-03-19 01:39:20,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6503/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6503/checkm_input OceanDNA-b6503/checkm_result
[2023-03-19 01:39:54,506] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:54,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:54,583] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:54,583] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:54,583] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6503/markers.fasta)
[2023-03-19 01:39:54,583] [INFO] Task started: Blastn
[2023-03-19 01:39:54,584] [INFO] Running command: blastn -query OceanDNA-b6503/markers.fasta -db /var/lib/cwl/stgb787a2c7-c339-47b2-86de-f42496974711/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6503/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:55,325] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:55,328] [INFO] Selected 18 target genomes.
[2023-03-19 01:39:55,328] [INFO] Target genome list was writen to OceanDNA-b6503/target_genomes_gtdb.txt
[2023-03-19 01:39:55,436] [INFO] Task started: fastANI
[2023-03-19 01:39:55,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ff4f13-3db6-4c91-998b-1bc712c7df3e/OceanDNA-b6503.fa --refList OceanDNA-b6503/target_genomes_gtdb.txt --output OceanDNA-b6503/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:40:08,579] [INFO] Task succeeded: fastANI
[2023-03-19 01:40:08,588] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:40:08,588] [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_002697475.1	s__Aquimarina sp002697475	93.0119	262	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216895.1	s__Aquimarina brevivitae	78.2664	192	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	77.3916	131	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430665.1	s__Aquimarina muelleri	77.2311	103	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000626715.1	s__Aquimarina atlantica	77.2262	114	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312815.1	s__Aquimarina sp900312815	77.1595	104	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299505.1	s__Aquimarina sp900299505	77.1196	120	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846555.1	s__Aquimarina sp002846555	77.1153	109	509	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	77.0889	97	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_016735115.1	s__Aquimarina mytili	77.0846	99	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013365535.1	s__Aquimarina sp013365535	77.0685	76	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370685.1	s__Aquimarina sp008370685	77.0107	91	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520955.1	s__Aquimarina pacifica	76.9438	84	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430645.1	s__Aquimarina latercula	76.9211	117	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_017897595.1	s__Aquimarina sp017897595	76.7314	81	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:40:08,591] [INFO] GTDB search result was written to OceanDNA-b6503/result_gtdb.tsv
[2023-03-19 01:40:08,594] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:40:08,597] [INFO] DFAST_QC result json was written to OceanDNA-b6503/dqc_result.json
[2023-03-19 01:40:08,597] [INFO] DFAST_QC completed!
[2023-03-19 01:40:08,597] [INFO] Total running time: 0h1m15s