[2024-01-24 12:06:33,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f512b36-3fb1-4a9e-bc7c-fbaf12438fe3/dqc_reference
[2024-01-24 12:06:34,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,714] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,714] [INFO] Running command: gunzip -c /var/lib/cwl/stgce81be22-3da0-4e85-8471-d19345f67fca/GCF_014637725.1_ASM1463772v1_genomic.fna.gz | prodigal -d GCF_014637725.1_ASM1463772v1_genomic.fna/cds.fna -a GCF_014637725.1_ASM1463772v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:50,180] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:50,180] [INFO] Task started: HMMsearch
[2024-01-24 12:06:50,180] [INFO] Running command: hmmsearch --tblout GCF_014637725.1_ASM1463772v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f512b36-3fb1-4a9e-bc7c-fbaf12438fe3/dqc_reference/reference_markers.hmm GCF_014637725.1_ASM1463772v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:50,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:50,459] [INFO] Found 6/6 markers.
[2024-01-24 12:06:50,504] [INFO] Query marker FASTA was written to GCF_014637725.1_ASM1463772v1_genomic.fna/markers.fasta
[2024-01-24 12:06:50,505] [INFO] Task started: Blastn
[2024-01-24 12:06:50,505] [INFO] Running command: blastn -query GCF_014637725.1_ASM1463772v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f512b36-3fb1-4a9e-bc7c-fbaf12438fe3/dqc_reference/reference_markers.fasta -out GCF_014637725.1_ASM1463772v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:51,606] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:51,611] [INFO] Selected 13 target genomes.
[2024-01-24 12:06:51,612] [INFO] Target genome list was writen to GCF_014637725.1_ASM1463772v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:51,621] [INFO] Task started: fastANI
[2024-01-24 12:06:51,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgce81be22-3da0-4e85-8471-d19345f67fca/GCF_014637725.1_ASM1463772v1_genomic.fna.gz --refList GCF_014637725.1_ASM1463772v1_genomic.fna/target_genomes.txt --output GCF_014637725.1_ASM1463772v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:03,082] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:03,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f512b36-3fb1-4a9e-bc7c-fbaf12438fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:03,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f512b36-3fb1-4a9e-bc7c-fbaf12438fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:03,099] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:03,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:03,100] [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
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	100.0	1559	1562	95	conclusive
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	83.6017	996	1562	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	82.6293	845	1562	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	82.6219	850	1562	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	80.0323	729	1562	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.8491	546	1562	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.4996	473	1562	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.1369	422	1562	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.097	400	1562	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	78.061	440	1562	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.0023	417	1562	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9916	408	1562	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.8703	426	1562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:03,101] [INFO] DFAST Taxonomy check result was written to GCF_014637725.1_ASM1463772v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:03,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:03,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:03,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f512b36-3fb1-4a9e-bc7c-fbaf12438fe3/dqc_reference/checkm_data
[2024-01-24 12:07:03,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:03,153] [INFO] Task started: CheckM
[2024-01-24 12:07:03,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637725.1_ASM1463772v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637725.1_ASM1463772v1_genomic.fna/checkm_input GCF_014637725.1_ASM1463772v1_genomic.fna/checkm_result
[2024-01-24 12:07:56,480] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:56,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,508] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:56,509] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:56,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637725.1_ASM1463772v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:56,509] [INFO] Task started: Blastn
[2024-01-24 12:07:56,510] [INFO] Running command: blastn -query GCF_014637725.1_ASM1463772v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f512b36-3fb1-4a9e-bc7c-fbaf12438fe3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637725.1_ASM1463772v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:58,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:58,508] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:58,508] [INFO] Target genome list was writen to GCF_014637725.1_ASM1463772v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:58,516] [INFO] Task started: fastANI
[2024-01-24 12:07:58,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgce81be22-3da0-4e85-8471-d19345f67fca/GCF_014637725.1_ASM1463772v1_genomic.fna.gz --refList GCF_014637725.1_ASM1463772v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637725.1_ASM1463772v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:08,690] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:08,703] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:08,703] [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_014637725.1	s__Marivita lacus	100.0	1559	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017643905.1	s__Marivita sp017643905	83.7309	924	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	83.5911	998	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_002115805.1	s__Marivita geojedonensis	82.6225	850	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003149565.1	s__Marivita sp003149565	81.7332	819	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129875.1	s__Marivita hallyeonensis	80.0243	730	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.5865	518	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	78.5194	488	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_000442255.1	s__Salipiger mucosus	78.3085	501	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:08,705] [INFO] GTDB search result was written to GCF_014637725.1_ASM1463772v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:08,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:08,708] [INFO] DFAST_QC result json was written to GCF_014637725.1_ASM1463772v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:08,708] [INFO] DFAST_QC completed!
[2024-01-24 12:08:08,708] [INFO] Total running time: 0h1m35s