[2023-03-15 16:15:00,881] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:15:00,881] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:15:00,881] [INFO] DQC Reference Directory: /var/lib/cwl/stgde1b9612-ef1f-41bd-bd22-2aed09b83aac/dqc_reference
[2023-03-15 16:15:01,994] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:15:01,994] [INFO] Task started: Prodigal
[2023-03-15 16:15:01,994] [INFO] Running command: cat /var/lib/cwl/stg608a860d-910f-45c9-8d99-6881f4f36c71/OceanDNA-b32607.fa | prodigal -d OceanDNA-b32607/cds.fna -a OceanDNA-b32607/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:10,660] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:10,660] [INFO] Task started: HMMsearch
[2023-03-15 16:15:10,660] [INFO] Running command: hmmsearch --tblout OceanDNA-b32607/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde1b9612-ef1f-41bd-bd22-2aed09b83aac/dqc_reference/reference_markers.hmm OceanDNA-b32607/protein.faa > /dev/null
[2023-03-15 16:15:10,819] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:10,820] [INFO] Found 6/6 markers.
[2023-03-15 16:15:10,834] [INFO] Query marker FASTA was written to OceanDNA-b32607/markers.fasta
[2023-03-15 16:15:10,835] [INFO] Task started: Blastn
[2023-03-15 16:15:10,835] [INFO] Running command: blastn -query OceanDNA-b32607/markers.fasta -db /var/lib/cwl/stgde1b9612-ef1f-41bd-bd22-2aed09b83aac/dqc_reference/reference_markers.fasta -out OceanDNA-b32607/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:11,466] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:11,467] [INFO] Selected 29 target genomes.
[2023-03-15 16:15:11,467] [INFO] Target genome list was writen to OceanDNA-b32607/target_genomes.txt
[2023-03-15 16:15:11,506] [INFO] Task started: fastANI
[2023-03-15 16:15:11,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg608a860d-910f-45c9-8d99-6881f4f36c71/OceanDNA-b32607.fa --refList OceanDNA-b32607/target_genomes.txt --output OceanDNA-b32607/fastani_result.tsv --threads 1
[2023-03-15 16:15:35,005] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:35,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde1b9612-ef1f-41bd-bd22-2aed09b83aac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:35,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde1b9612-ef1f-41bd-bd22-2aed09b83aac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:35,012] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:15:35,012] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:15:35,012] [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
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.1274	50	392	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.7262	52	392	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.6784	53	392	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.6559	52	392	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.5489	54	392	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.4292	57	392	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.3252	50	392	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:15:35,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32607/tc_result.tsv
[2023-03-15 16:15:35,012] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:35,012] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:35,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde1b9612-ef1f-41bd-bd22-2aed09b83aac/dqc_reference/checkm_data
[2023-03-15 16:15:35,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:35,016] [INFO] Task started: CheckM
[2023-03-15 16:15:35,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32607/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32607/checkm_input OceanDNA-b32607/checkm_result
[2023-03-15 16:16:01,697] [INFO] Task succeeded: CheckM
[2023-03-15 16:16:01,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 16:16:01,735] [INFO] ===== Completeness check finished =====
[2023-03-15 16:16:01,735] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:16:01,735] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32607/markers.fasta)
[2023-03-15 16:16:01,735] [INFO] Task started: Blastn
[2023-03-15 16:16:01,735] [INFO] Running command: blastn -query OceanDNA-b32607/markers.fasta -db /var/lib/cwl/stgde1b9612-ef1f-41bd-bd22-2aed09b83aac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32607/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:16:02,799] [INFO] Task succeeded: Blastn
[2023-03-15 16:16:02,804] [INFO] Selected 27 target genomes.
[2023-03-15 16:16:02,804] [INFO] Target genome list was writen to OceanDNA-b32607/target_genomes_gtdb.txt
[2023-03-15 16:16:02,963] [INFO] Task started: fastANI
[2023-03-15 16:16:02,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg608a860d-910f-45c9-8d99-6881f4f36c71/OceanDNA-b32607.fa --refList OceanDNA-b32607/target_genomes_gtdb.txt --output OceanDNA-b32607/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:16:21,587] [INFO] Task succeeded: fastANI
[2023-03-15 16:16:21,592] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:16:21,592] [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_009380075.1	s__WHSO01 sp009380075	78.4686	204	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__WHSO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356985.1	s__SMXQ01 sp004356985	77.0957	112	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.0027	53	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	75.9767	52	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_004923295.1	s__Azospirillum sp003115975	75.9355	56	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	75.6804	51	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423485.1	s__Azospirillum oleiclasticum	75.6784	53	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900230255.1	s__Caenispirillum bisanense	75.4264	54	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:16:21,593] [INFO] GTDB search result was written to OceanDNA-b32607/result_gtdb.tsv
[2023-03-15 16:16:21,593] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:16:21,594] [INFO] DFAST_QC result json was written to OceanDNA-b32607/dqc_result.json
[2023-03-15 16:16:21,594] [INFO] DFAST_QC completed!
[2023-03-15 16:16:21,594] [INFO] Total running time: 0h1m21s