[2023-03-15 05:53:02,294] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:53:02,294] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:53:02,294] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb4ca9e6-0a44-4786-868d-446d94127a86/dqc_reference
[2023-03-15 05:53:03,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:53:03,416] [INFO] Task started: Prodigal
[2023-03-15 05:53:03,416] [INFO] Running command: cat /var/lib/cwl/stga061b677-0bdb-4168-a1df-d0601d998400/OceanDNA-b46651.fa | prodigal -d OceanDNA-b46651/cds.fna -a OceanDNA-b46651/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:53:44,338] [INFO] Task succeeded: Prodigal
[2023-03-15 05:53:44,338] [INFO] Task started: HMMsearch
[2023-03-15 05:53:44,339] [INFO] Running command: hmmsearch --tblout OceanDNA-b46651/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb4ca9e6-0a44-4786-868d-446d94127a86/dqc_reference/reference_markers.hmm OceanDNA-b46651/protein.faa > /dev/null
[2023-03-15 05:53:44,579] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:53:44,580] [INFO] Found 6/6 markers.
[2023-03-15 05:53:44,617] [INFO] Query marker FASTA was written to OceanDNA-b46651/markers.fasta
[2023-03-15 05:53:44,618] [INFO] Task started: Blastn
[2023-03-15 05:53:44,618] [INFO] Running command: blastn -query OceanDNA-b46651/markers.fasta -db /var/lib/cwl/stgcb4ca9e6-0a44-4786-868d-446d94127a86/dqc_reference/reference_markers.fasta -out OceanDNA-b46651/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:45,167] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:45,171] [INFO] Selected 21 target genomes.
[2023-03-15 05:53:45,171] [INFO] Target genome list was writen to OceanDNA-b46651/target_genomes.txt
[2023-03-15 05:53:45,183] [INFO] Task started: fastANI
[2023-03-15 05:53:45,183] [INFO] Running command: fastANI --query /var/lib/cwl/stga061b677-0bdb-4168-a1df-d0601d998400/OceanDNA-b46651.fa --refList OceanDNA-b46651/target_genomes.txt --output OceanDNA-b46651/fastani_result.tsv --threads 1
[2023-03-15 05:53:58,524] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:58,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb4ca9e6-0a44-4786-868d-446d94127a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:53:58,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb4ca9e6-0a44-4786-868d-446d94127a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:53:58,529] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:53:58,529] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:53:58,529] [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
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.4122	69	1375	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.9377	79	1375	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.6377	61	1375	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:53:58,531] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46651/tc_result.tsv
[2023-03-15 05:53:58,532] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:53:58,532] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:53:58,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb4ca9e6-0a44-4786-868d-446d94127a86/dqc_reference/checkm_data
[2023-03-15 05:53:58,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:53:58,542] [INFO] Task started: CheckM
[2023-03-15 05:53:58,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46651/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46651/checkm_input OceanDNA-b46651/checkm_result
[2023-03-15 05:55:37,017] [INFO] Task succeeded: CheckM
[2023-03-15 05:55:37,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:55:37,063] [INFO] ===== Completeness check finished =====
[2023-03-15 05:55:37,063] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:55:37,063] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46651/markers.fasta)
[2023-03-15 05:55:37,064] [INFO] Task started: Blastn
[2023-03-15 05:55:37,064] [INFO] Running command: blastn -query OceanDNA-b46651/markers.fasta -db /var/lib/cwl/stgcb4ca9e6-0a44-4786-868d-446d94127a86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46651/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:55:38,032] [INFO] Task succeeded: Blastn
[2023-03-15 05:55:38,038] [INFO] Selected 14 target genomes.
[2023-03-15 05:55:38,038] [INFO] Target genome list was writen to OceanDNA-b46651/target_genomes_gtdb.txt
[2023-03-15 05:55:38,066] [INFO] Task started: fastANI
[2023-03-15 05:55:38,066] [INFO] Running command: fastANI --query /var/lib/cwl/stga061b677-0bdb-4168-a1df-d0601d998400/OceanDNA-b46651.fa --refList OceanDNA-b46651/target_genomes_gtdb.txt --output OceanDNA-b46651/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:55:47,401] [INFO] Task succeeded: fastANI
[2023-03-15 05:55:47,407] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:55:47,407] [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_003483645.1	s__Roseibacillus_B sp003483645	78.8004	239	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	78.5114	235	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501065.1	s__Roseibacillus_B sp002501065	78.3982	358	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	76.9465	251	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	76.7832	187	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595525.1	s__Haloferula rosea	76.4122	69	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723015.1	s__Roseibacillus_B sp002723015	76.2024	60	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.32	99.32	0.93	0.93	2	-
GCF_018137965.1	s__Luteolibacter sp018137965	75.9733	77	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	75.9099	102	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	75.8815	55	1375	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:55:47,410] [INFO] GTDB search result was written to OceanDNA-b46651/result_gtdb.tsv
[2023-03-15 05:55:47,413] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:55:47,416] [INFO] DFAST_QC result json was written to OceanDNA-b46651/dqc_result.json
[2023-03-15 05:55:47,416] [INFO] DFAST_QC completed!
[2023-03-15 05:55:47,416] [INFO] Total running time: 0h2m45s