[2023-03-16 04:05:20,426] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,426] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg35fc3358-3d0e-49ac-917d-21113f8b6fab/dqc_reference
[2023-03-16 04:05:22,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,127] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,127] [INFO] Running command: cat /var/lib/cwl/stg37a5fe7f-4cd6-4c52-bc4d-eb66a17c1594/OceanDNA-b46819.fa | prodigal -d OceanDNA-b46819/cds.fna -a OceanDNA-b46819/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:06:12,302] [INFO] Task succeeded: Prodigal
[2023-03-16 04:06:12,303] [INFO] Task started: HMMsearch
[2023-03-16 04:06:12,303] [INFO] Running command: hmmsearch --tblout OceanDNA-b46819/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35fc3358-3d0e-49ac-917d-21113f8b6fab/dqc_reference/reference_markers.hmm OceanDNA-b46819/protein.faa > /dev/null
[2023-03-16 04:06:12,552] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:06:12,553] [INFO] Found 6/6 markers.
[2023-03-16 04:06:12,589] [INFO] Query marker FASTA was written to OceanDNA-b46819/markers.fasta
[2023-03-16 04:06:12,589] [INFO] Task started: Blastn
[2023-03-16 04:06:12,589] [INFO] Running command: blastn -query OceanDNA-b46819/markers.fasta -db /var/lib/cwl/stg35fc3358-3d0e-49ac-917d-21113f8b6fab/dqc_reference/reference_markers.fasta -out OceanDNA-b46819/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:13,108] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:13,109] [INFO] Selected 19 target genomes.
[2023-03-16 04:06:13,109] [INFO] Target genome list was writen to OceanDNA-b46819/target_genomes.txt
[2023-03-16 04:06:13,118] [INFO] Task started: fastANI
[2023-03-16 04:06:13,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg37a5fe7f-4cd6-4c52-bc4d-eb66a17c1594/OceanDNA-b46819.fa --refList OceanDNA-b46819/target_genomes.txt --output OceanDNA-b46819/fastani_result.tsv --threads 1
[2023-03-16 04:06:26,424] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:26,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35fc3358-3d0e-49ac-917d-21113f8b6fab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:26,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35fc3358-3d0e-49ac-917d-21113f8b6fab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:26,429] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:26,429] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:06:26,429] [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
Roseibacillus persicicus	strain=KCTC 12988	GCA_014651675.1	454148	454148	type	True	76.8858	72	1859	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.3641	50	1859	95	below_threshold
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	76.2264	84	1859	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.8669	57	1859	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.6558	61	1859	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:06:26,429] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46819/tc_result.tsv
[2023-03-16 04:06:26,430] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:26,430] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:26,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35fc3358-3d0e-49ac-917d-21113f8b6fab/dqc_reference/checkm_data
[2023-03-16 04:06:26,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:26,524] [INFO] Task started: CheckM
[2023-03-16 04:06:26,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46819/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46819/checkm_input OceanDNA-b46819/checkm_result
[2023-03-16 04:08:28,878] [INFO] Task succeeded: CheckM
[2023-03-16 04:08:28,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:08:28,882] [INFO] ===== Completeness check finished =====
[2023-03-16 04:08:28,882] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:08:28,882] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46819/markers.fasta)
[2023-03-16 04:08:28,883] [INFO] Task started: Blastn
[2023-03-16 04:08:28,883] [INFO] Running command: blastn -query OceanDNA-b46819/markers.fasta -db /var/lib/cwl/stg35fc3358-3d0e-49ac-917d-21113f8b6fab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46819/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:08:29,612] [INFO] Task succeeded: Blastn
[2023-03-16 04:08:29,613] [INFO] Selected 17 target genomes.
[2023-03-16 04:08:29,614] [INFO] Target genome list was writen to OceanDNA-b46819/target_genomes_gtdb.txt
[2023-03-16 04:08:29,788] [INFO] Task started: fastANI
[2023-03-16 04:08:29,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg37a5fe7f-4cd6-4c52-bc4d-eb66a17c1594/OceanDNA-b46819.fa --refList OceanDNA-b46819/target_genomes_gtdb.txt --output OceanDNA-b46819/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:08:39,176] [INFO] Task succeeded: fastANI
[2023-03-16 04:08:39,183] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:08:39,184] [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_905182405.1	s__SW10 sp905182405	79.5826	322	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222765.1	s__SW10 sp018222765	77.9777	272	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172625.1	s__SW10 sp002172625	77.8682	231	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
GCA_002729295.1	s__SW10 sp002729295	77.74	208	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCA_905181965.1	s__SW10 sp905181965	77.4457	154	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.78	97.70	0.75	0.63	5	-
GCA_002323895.1	s__SW10 sp002323895	77.4439	187	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.17	98.66	0.86	0.81	3	-
GCA_000383735.1	s__SW10 sp000383735	77.3637	127	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478925.1	s__Luteolibacter sp905478925	77.1672	80	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	97.95	97.95	0.92	0.92	2	-
GCA_002420315.1	s__SW10 sp002420315	77.1594	183	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.54	96.31	0.84	0.80	11	-
GCA_004293445.1	s__Haloferula sp004293445	76.1815	56	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	99.99	99.98	0.97	0.96	4	-
GCF_014904755.1	s__Haloferula sp014904755	75.8262	75	1859	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:08:39,184] [INFO] GTDB search result was written to OceanDNA-b46819/result_gtdb.tsv
[2023-03-16 04:08:39,184] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:08:39,185] [INFO] DFAST_QC result json was written to OceanDNA-b46819/dqc_result.json
[2023-03-16 04:08:39,185] [INFO] DFAST_QC completed!
[2023-03-16 04:08:39,185] [INFO] Total running time: 0h3m19s