[2023-03-16 00:42:12,744] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:42:12,744] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:42:12,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a9be92a-d8b0-406c-ad40-a2d9da57cf54/dqc_reference
[2023-03-16 00:42:14,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:42:14,523] [INFO] Task started: Prodigal
[2023-03-16 00:42:14,523] [INFO] Running command: cat /var/lib/cwl/stg428e1ba6-b14c-4a2e-b856-634b7041f2e2/OceanDNA-b46871.fa | prodigal -d OceanDNA-b46871/cds.fna -a OceanDNA-b46871/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:42:27,303] [INFO] Task succeeded: Prodigal
[2023-03-16 00:42:27,303] [INFO] Task started: HMMsearch
[2023-03-16 00:42:27,303] [INFO] Running command: hmmsearch --tblout OceanDNA-b46871/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a9be92a-d8b0-406c-ad40-a2d9da57cf54/dqc_reference/reference_markers.hmm OceanDNA-b46871/protein.faa > /dev/null
[2023-03-16 00:42:27,470] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:42:27,470] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg428e1ba6-b14c-4a2e-b856-634b7041f2e2/OceanDNA-b46871.fa]
[2023-03-16 00:42:27,485] [INFO] Query marker FASTA was written to OceanDNA-b46871/markers.fasta
[2023-03-16 00:42:27,486] [INFO] Task started: Blastn
[2023-03-16 00:42:27,486] [INFO] Running command: blastn -query OceanDNA-b46871/markers.fasta -db /var/lib/cwl/stg9a9be92a-d8b0-406c-ad40-a2d9da57cf54/dqc_reference/reference_markers.fasta -out OceanDNA-b46871/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:42:28,001] [INFO] Task succeeded: Blastn
[2023-03-16 00:42:28,002] [INFO] Selected 22 target genomes.
[2023-03-16 00:42:28,002] [INFO] Target genome list was writen to OceanDNA-b46871/target_genomes.txt
[2023-03-16 00:42:28,015] [INFO] Task started: fastANI
[2023-03-16 00:42:28,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg428e1ba6-b14c-4a2e-b856-634b7041f2e2/OceanDNA-b46871.fa --refList OceanDNA-b46871/target_genomes.txt --output OceanDNA-b46871/fastani_result.tsv --threads 1
[2023-03-16 00:42:42,868] [INFO] Task succeeded: fastANI
[2023-03-16 00:42:42,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a9be92a-d8b0-406c-ad40-a2d9da57cf54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:42:42,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a9be92a-d8b0-406c-ad40-a2d9da57cf54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:42:42,872] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:42:42,872] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:42:42,872] [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
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	77.3354	81	406	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.2289	102	406	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.9031	65	406	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:42:42,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46871/tc_result.tsv
[2023-03-16 00:42:42,873] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:42:42,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:42:42,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a9be92a-d8b0-406c-ad40-a2d9da57cf54/dqc_reference/checkm_data
[2023-03-16 00:42:42,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:42:42,913] [INFO] Task started: CheckM
[2023-03-16 00:42:42,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46871/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46871/checkm_input OceanDNA-b46871/checkm_result
[2023-03-16 00:43:19,402] [INFO] Task succeeded: CheckM
[2023-03-16 00:43:19,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:43:19,406] [INFO] ===== Completeness check finished =====
[2023-03-16 00:43:19,406] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:43:19,406] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46871/markers.fasta)
[2023-03-16 00:43:19,407] [INFO] Task started: Blastn
[2023-03-16 00:43:19,407] [INFO] Running command: blastn -query OceanDNA-b46871/markers.fasta -db /var/lib/cwl/stg9a9be92a-d8b0-406c-ad40-a2d9da57cf54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46871/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:43:20,128] [INFO] Task succeeded: Blastn
[2023-03-16 00:43:20,130] [INFO] Selected 13 target genomes.
[2023-03-16 00:43:20,130] [INFO] Target genome list was writen to OceanDNA-b46871/target_genomes_gtdb.txt
[2023-03-16 00:43:20,144] [INFO] Task started: fastANI
[2023-03-16 00:43:20,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg428e1ba6-b14c-4a2e-b856-634b7041f2e2/OceanDNA-b46871.fa --refList OceanDNA-b46871/target_genomes_gtdb.txt --output OceanDNA-b46871/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:43:28,450] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:28,457] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:43:28,457] [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_905478925.1	s__Luteolibacter sp905478925	98.0032	383	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	97.95	97.95	0.92	0.92	2	conclusive
GCA_017798145.1	s__Luteolibacter sp017798145	80.3648	286	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182475.1	s__Luteolibacter sp905182475	79.9718	211	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.83	99.83	0.94	0.94	2	-
GCA_018402445.1	s__Luteolibacter sp018402445	79.0138	224	406	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	77.641	86	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379305.1	s__Luteolibacter sp014379305	77.4211	63	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	77.369	80	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003820635.1	s__Luteolibacter sp003820635	77.3008	101	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	77.229	54	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969605.1	s__Luteolibacter sp018969605	76.4653	59	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934285.1	s__Luteolibacter sp903934285	76.2871	54	406	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.86	99.86	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-16 00:43:28,461] [INFO] GTDB search result was written to OceanDNA-b46871/result_gtdb.tsv
[2023-03-16 00:43:28,466] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:43:28,469] [INFO] DFAST_QC result json was written to OceanDNA-b46871/dqc_result.json
[2023-03-16 00:43:28,469] [INFO] DFAST_QC completed!
[2023-03-16 00:43:28,470] [INFO] Total running time: 0h1m16s