[2023-03-17 07:44:36,993] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,993] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,993] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb60415a-3e25-4393-85bb-b357098b67a2/dqc_reference
[2023-03-17 07:44:38,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,850] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,850] [INFO] Running command: cat /var/lib/cwl/stg91d40617-8c9e-4e57-bd7b-a8621ab80deb/OceanDNA-b46688.fa | prodigal -d OceanDNA-b46688/cds.fna -a OceanDNA-b46688/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:45:09,738] [INFO] Task succeeded: Prodigal
[2023-03-17 07:45:09,738] [INFO] Task started: HMMsearch
[2023-03-17 07:45:09,739] [INFO] Running command: hmmsearch --tblout OceanDNA-b46688/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb60415a-3e25-4393-85bb-b357098b67a2/dqc_reference/reference_markers.hmm OceanDNA-b46688/protein.faa > /dev/null
[2023-03-17 07:45:09,955] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:45:09,956] [INFO] Found 6/6 markers.
[2023-03-17 07:45:09,981] [INFO] Query marker FASTA was written to OceanDNA-b46688/markers.fasta
[2023-03-17 07:45:09,981] [INFO] Task started: Blastn
[2023-03-17 07:45:09,981] [INFO] Running command: blastn -query OceanDNA-b46688/markers.fasta -db /var/lib/cwl/stgdb60415a-3e25-4393-85bb-b357098b67a2/dqc_reference/reference_markers.fasta -out OceanDNA-b46688/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:10,510] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:10,511] [INFO] Selected 17 target genomes.
[2023-03-17 07:45:10,511] [INFO] Target genome list was writen to OceanDNA-b46688/target_genomes.txt
[2023-03-17 07:45:10,522] [INFO] Task started: fastANI
[2023-03-17 07:45:10,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg91d40617-8c9e-4e57-bd7b-a8621ab80deb/OceanDNA-b46688.fa --refList OceanDNA-b46688/target_genomes.txt --output OceanDNA-b46688/fastani_result.tsv --threads 1
[2023-03-17 07:45:24,489] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:24,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb60415a-3e25-4393-85bb-b357098b67a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:24,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb60415a-3e25-4393-85bb-b357098b67a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:24,495] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:24,495] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:45:24,495] [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 luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	77.4893	256	1213	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	77.2531	113	1213	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.6646	139	1213	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	76.6299	97	1213	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	76.2325	91	1213	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:45:24,495] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46688/tc_result.tsv
[2023-03-17 07:45:24,495] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:24,495] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:24,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb60415a-3e25-4393-85bb-b357098b67a2/dqc_reference/checkm_data
[2023-03-17 07:45:24,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:24,627] [INFO] Task started: CheckM
[2023-03-17 07:45:24,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46688/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46688/checkm_input OceanDNA-b46688/checkm_result
[2023-03-17 07:46:42,730] [INFO] Task succeeded: CheckM
[2023-03-17 07:46:42,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:46:42,733] [INFO] ===== Completeness check finished =====
[2023-03-17 07:46:42,733] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:46:42,734] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46688/markers.fasta)
[2023-03-17 07:46:42,734] [INFO] Task started: Blastn
[2023-03-17 07:46:42,734] [INFO] Running command: blastn -query OceanDNA-b46688/markers.fasta -db /var/lib/cwl/stgdb60415a-3e25-4393-85bb-b357098b67a2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46688/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:46:43,456] [INFO] Task succeeded: Blastn
[2023-03-17 07:46:43,457] [INFO] Selected 14 target genomes.
[2023-03-17 07:46:43,457] [INFO] Target genome list was writen to OceanDNA-b46688/target_genomes_gtdb.txt
[2023-03-17 07:46:43,518] [INFO] Task started: fastANI
[2023-03-17 07:46:43,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg91d40617-8c9e-4e57-bd7b-a8621ab80deb/OceanDNA-b46688.fa --refList OceanDNA-b46688/target_genomes_gtdb.txt --output OceanDNA-b46688/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:46:54,097] [INFO] Task succeeded: fastANI
[2023-03-17 07:46:54,102] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:46:54,103] [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_014904755.1	s__Haloferula sp014904755	78.4121	468	1213	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	77.5003	255	1213	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	77.2167	245	1213	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	77.1428	238	1213	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293445.1	s__Haloferula sp004293445	77.0867	211	1213	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	99.99	99.98	0.97	0.96	4	-
GCF_016595465.1	s__Luteolibacter yonseiensis	76.6299	97	1213	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919975.1	s__Luteolibacter sp903919975	76.4096	69	1213	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.84	0.96	0.96	3	-
GCA_903908495.1	s__Luteolibacter sp903908495	75.7376	57	1213	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:46:54,103] [INFO] GTDB search result was written to OceanDNA-b46688/result_gtdb.tsv
[2023-03-17 07:46:54,103] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:46:54,104] [INFO] DFAST_QC result json was written to OceanDNA-b46688/dqc_result.json
[2023-03-17 07:46:54,104] [INFO] DFAST_QC completed!
[2023-03-17 07:46:54,104] [INFO] Total running time: 0h2m17s