[2024-01-25 18:48:35,513] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg34b240f8-1e99-42ec-a9c9-9a5274b9b813/dqc_reference
[2024-01-25 18:48:36,701] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:36,702] [INFO] Task started: Prodigal
[2024-01-25 18:48:36,702] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc87eb23-1a7c-4d7d-a9da-fad8f98451b9/GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:48,615] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:48,615] [INFO] Task started: HMMsearch
[2024-01-25 18:48:48,615] [INFO] Running command: hmmsearch --tblout GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34b240f8-1e99-42ec-a9c9-9a5274b9b813/dqc_reference/reference_markers.hmm GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:48,912] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:48,914] [INFO] Found 6/6 markers.
[2024-01-25 18:48:48,958] [INFO] Query marker FASTA was written to GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta
[2024-01-25 18:48:48,959] [INFO] Task started: Blastn
[2024-01-25 18:48:48,959] [INFO] Running command: blastn -query GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg34b240f8-1e99-42ec-a9c9-9a5274b9b813/dqc_reference/reference_markers.fasta -out GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:50,008] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:50,010] [INFO] Selected 16 target genomes.
[2024-01-25 18:48:50,010] [INFO] Target genome list was writen to GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt
[2024-01-25 18:48:50,022] [INFO] Task started: fastANI
[2024-01-25 18:48:50,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc87eb23-1a7c-4d7d-a9da-fad8f98451b9/GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:04,875] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:04,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34b240f8-1e99-42ec-a9c9-9a5274b9b813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:04,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34b240f8-1e99-42ec-a9c9-9a5274b9b813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:04,887] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:04,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:04,887] [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
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	100.0	1542	1552	95	conclusive
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	81.7757	823	1552	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	81.5949	824	1552	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	81.5596	847	1552	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	80.4728	771	1552	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	80.2068	722	1552	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.1451	718	1552	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.5458	720	1552	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.5252	716	1552	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	79.4302	609	1552	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	79.057	570	1552	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.0469	556	1552	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.9569	637	1552	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.5835	488	1552	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4189	492	1552	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7878	430	1552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:04,893] [INFO] DFAST Taxonomy check result was written to GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv
[2024-01-25 18:49:04,894] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:04,894] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:04,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34b240f8-1e99-42ec-a9c9-9a5274b9b813/dqc_reference/checkm_data
[2024-01-25 18:49:04,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:04,943] [INFO] Task started: CheckM
[2024-01-25 18:49:04,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/checkm_result
[2024-01-25 18:50:05,390] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:05,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:05,439] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:05,440] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:05,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta)
[2024-01-25 18:50:05,441] [INFO] Task started: Blastn
[2024-01-25 18:50:05,441] [INFO] Running command: blastn -query GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg34b240f8-1e99-42ec-a9c9-9a5274b9b813/dqc_reference/reference_markers_gtdb.fasta -out GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:07,637] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:07,639] [INFO] Selected 12 target genomes.
[2024-01-25 18:50:07,639] [INFO] Target genome list was writen to GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:07,649] [INFO] Task started: fastANI
[2024-01-25 18:50:07,649] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc87eb23-1a7c-4d7d-a9da-fad8f98451b9/GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:19,763] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:19,771] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:19,772] [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_000521865.1	s__Roseivivax isoporae	100.0	1542	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000521785.1	s__Roseivivax halodurans	81.7823	823	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112685.1	s__Roseivivax sediminis	81.7071	862	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	81.587	825	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_900172265.1	s__Roseivivax jejudonensis	81.5805	842	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	80.48	770	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	80.4071	760	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	80.2142	721	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_002814095.1	s__Sagittula sp002814095	79.6014	685	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.4572	618	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	79.0609	569	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	78.8559	553	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:19,773] [INFO] GTDB search result was written to GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:19,774] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:19,776] [INFO] DFAST_QC result json was written to GCF_000521865.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json
[2024-01-25 18:50:19,777] [INFO] DFAST_QC completed!
[2024-01-25 18:50:19,777] [INFO] Total running time: 0h1m44s