[2024-01-24 13:01:23,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:23,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:23,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg20b7ba8a-0d65-4c42-9344-85840a32c9b3/dqc_reference
[2024-01-24 13:01:24,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:24,525] [INFO] Task started: Prodigal
[2024-01-24 13:01:24,526] [INFO] Running command: gunzip -c /var/lib/cwl/stg62511308-b63b-46a5-b095-10e4b61ccaf3/GCF_008368715.1_ASM836871v1_genomic.fna.gz | prodigal -d GCF_008368715.1_ASM836871v1_genomic.fna/cds.fna -a GCF_008368715.1_ASM836871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:32,199] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:32,199] [INFO] Task started: HMMsearch
[2024-01-24 13:01:32,199] [INFO] Running command: hmmsearch --tblout GCF_008368715.1_ASM836871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20b7ba8a-0d65-4c42-9344-85840a32c9b3/dqc_reference/reference_markers.hmm GCF_008368715.1_ASM836871v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:32,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:32,460] [INFO] Found 6/6 markers.
[2024-01-24 13:01:32,487] [INFO] Query marker FASTA was written to GCF_008368715.1_ASM836871v1_genomic.fna/markers.fasta
[2024-01-24 13:01:32,487] [INFO] Task started: Blastn
[2024-01-24 13:01:32,488] [INFO] Running command: blastn -query GCF_008368715.1_ASM836871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20b7ba8a-0d65-4c42-9344-85840a32c9b3/dqc_reference/reference_markers.fasta -out GCF_008368715.1_ASM836871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:33,129] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:33,132] [INFO] Selected 28 target genomes.
[2024-01-24 13:01:33,132] [INFO] Target genome list was writen to GCF_008368715.1_ASM836871v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:33,152] [INFO] Task started: fastANI
[2024-01-24 13:01:33,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg62511308-b63b-46a5-b095-10e4b61ccaf3/GCF_008368715.1_ASM836871v1_genomic.fna.gz --refList GCF_008368715.1_ASM836871v1_genomic.fna/target_genomes.txt --output GCF_008368715.1_ASM836871v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:50,517] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:50,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20b7ba8a-0d65-4c42-9344-85840a32c9b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:50,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20b7ba8a-0d65-4c42-9344-85840a32c9b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:50,531] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:50,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:50,532] [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
Nitrincola tapanii	strain=MEB193	GCA_008368715.1	1708751	1708751	type	True	100.0	921	921	95	conclusive
Nitrincola schmidtii	strain=NCAIM B.02626	GCA_008973715.1	1730894	1730894	type	True	78.4159	144	921	95	below_threshold
Nitrincola tibetensis	strain=xg18	GCA_003284585.1	2219697	2219697	type	True	78.3985	121	921	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	78.2587	171	921	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	78.1842	60	921	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	78.1068	96	921	95	below_threshold
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	78.023	61	921	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	77.7997	184	921	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	77.7707	96	921	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	77.7561	95	921	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	77.7533	96	921	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	77.4634	57	921	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	77.1714	72	921	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	77.0506	88	921	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	77.0496	72	921	95	below_threshold
Neptuniibacter marinus	strain=ATR 1.1	GCA_001597725.1	1806670	1806670	type	True	76.2069	53	921	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:50,533] [INFO] DFAST Taxonomy check result was written to GCF_008368715.1_ASM836871v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:50,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:50,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:50,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20b7ba8a-0d65-4c42-9344-85840a32c9b3/dqc_reference/checkm_data
[2024-01-24 13:01:50,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:50,567] [INFO] Task started: CheckM
[2024-01-24 13:01:50,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008368715.1_ASM836871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008368715.1_ASM836871v1_genomic.fna/checkm_input GCF_008368715.1_ASM836871v1_genomic.fna/checkm_result
[2024-01-24 13:02:19,034] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:19,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,054] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:19,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:19,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008368715.1_ASM836871v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:19,055] [INFO] Task started: Blastn
[2024-01-24 13:02:19,056] [INFO] Running command: blastn -query GCF_008368715.1_ASM836871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20b7ba8a-0d65-4c42-9344-85840a32c9b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008368715.1_ASM836871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:19,949] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:19,953] [INFO] Selected 24 target genomes.
[2024-01-24 13:02:19,954] [INFO] Target genome list was writen to GCF_008368715.1_ASM836871v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:19,972] [INFO] Task started: fastANI
[2024-01-24 13:02:19,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg62511308-b63b-46a5-b095-10e4b61ccaf3/GCF_008368715.1_ASM836871v1_genomic.fna.gz --refList GCF_008368715.1_ASM836871v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008368715.1_ASM836871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:34,686] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:34,710] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:34,710] [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_008368715.1	s__Nitrincola tapanii	100.0	921	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003284585.1	s__Nitrincola tibetensis	78.4289	120	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973715.1	s__Nitrincola schmidtii	78.4131	142	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009821115.1	s__Nitrincola alkalisediminis	78.2895	140	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	99.09	99.09	0.91	0.91	2	-
GCF_000691225.1	s__Nitrincola lacisaponensis	78.2587	171	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630635.1	s__Neptunomonas concharum	78.023	61	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000764495.1	s__Nitrincola sp000764495	77.9235	156	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000705555.1	s__Marinobacterium sp000705555	77.8469	83	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.11	98.11	0.90	0.90	2	-
GCF_008727795.1	s__Nitrincola sp008727795	77.7929	183	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155945.1	s__Marinobacterium stanieri	77.7707	96	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCF_900108065.1	s__Marinobacterium lutimaris	77.7517	95	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693685.1	s__Nitrincola sp007693685	77.372	115	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	77.2063	84	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957515.1	s__Amphritea opalescens	77.1714	72	921	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,712] [INFO] GTDB search result was written to GCF_008368715.1_ASM836871v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:34,712] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:34,716] [INFO] DFAST_QC result json was written to GCF_008368715.1_ASM836871v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:34,716] [INFO] DFAST_QC completed!
[2024-01-24 13:02:34,716] [INFO] Total running time: 0h1m12s