[2024-01-24 14:39:00,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:00,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:00,318] [INFO] DQC Reference Directory: /var/lib/cwl/stge1b764d8-2a18-454d-918b-e6fc9c71184c/dqc_reference
[2024-01-24 14:39:01,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:01,634] [INFO] Task started: Prodigal
[2024-01-24 14:39:01,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg49c07c01-43b6-4540-bd33-d49edc01e2e9/GCF_007992495.1_ASM799249v1_genomic.fna.gz | prodigal -d GCF_007992495.1_ASM799249v1_genomic.fna/cds.fna -a GCF_007992495.1_ASM799249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:29,981] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:29,981] [INFO] Task started: HMMsearch
[2024-01-24 14:39:29,982] [INFO] Running command: hmmsearch --tblout GCF_007992495.1_ASM799249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1b764d8-2a18-454d-918b-e6fc9c71184c/dqc_reference/reference_markers.hmm GCF_007992495.1_ASM799249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:30,431] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:30,432] [INFO] Found 6/6 markers.
[2024-01-24 14:39:30,509] [INFO] Query marker FASTA was written to GCF_007992495.1_ASM799249v1_genomic.fna/markers.fasta
[2024-01-24 14:39:30,509] [INFO] Task started: Blastn
[2024-01-24 14:39:30,509] [INFO] Running command: blastn -query GCF_007992495.1_ASM799249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b764d8-2a18-454d-918b-e6fc9c71184c/dqc_reference/reference_markers.fasta -out GCF_007992495.1_ASM799249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:31,574] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:31,578] [INFO] Selected 15 target genomes.
[2024-01-24 14:39:31,578] [INFO] Target genome list was writen to GCF_007992495.1_ASM799249v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:31,584] [INFO] Task started: fastANI
[2024-01-24 14:39:31,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg49c07c01-43b6-4540-bd33-d49edc01e2e9/GCF_007992495.1_ASM799249v1_genomic.fna.gz --refList GCF_007992495.1_ASM799249v1_genomic.fna/target_genomes.txt --output GCF_007992495.1_ASM799249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:54,717] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:54,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1b764d8-2a18-454d-918b-e6fc9c71184c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:54,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1b764d8-2a18-454d-918b-e6fc9c71184c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:54,731] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:54,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:54,732] [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
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	100.0	3075	3090	95	conclusive
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	82.654	1289	3090	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	82.3436	1260	3090	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	79.3407	1113	3090	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.027	581	3090	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.723	539	3090	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.6748	508	3090	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.6746	636	3090	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.649	676	3090	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.6326	410	3090	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.5243	339	3090	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.3521	371	3090	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	76.2993	295	3090	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.1531	395	3090	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.935	257	3090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:54,733] [INFO] DFAST Taxonomy check result was written to GCF_007992495.1_ASM799249v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:54,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:54,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:54,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1b764d8-2a18-454d-918b-e6fc9c71184c/dqc_reference/checkm_data
[2024-01-24 14:39:54,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:54,830] [INFO] Task started: CheckM
[2024-01-24 14:39:54,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992495.1_ASM799249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992495.1_ASM799249v1_genomic.fna/checkm_input GCF_007992495.1_ASM799249v1_genomic.fna/checkm_result
[2024-01-24 14:41:15,975] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:15,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:16,004] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:16,004] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:16,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992495.1_ASM799249v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:16,005] [INFO] Task started: Blastn
[2024-01-24 14:41:16,005] [INFO] Running command: blastn -query GCF_007992495.1_ASM799249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b764d8-2a18-454d-918b-e6fc9c71184c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992495.1_ASM799249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:18,063] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:18,067] [INFO] Selected 11 target genomes.
[2024-01-24 14:41:18,068] [INFO] Target genome list was writen to GCF_007992495.1_ASM799249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:18,079] [INFO] Task started: fastANI
[2024-01-24 14:41:18,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg49c07c01-43b6-4540-bd33-d49edc01e2e9/GCF_007992495.1_ASM799249v1_genomic.fna.gz --refList GCF_007992495.1_ASM799249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992495.1_ASM799249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:39,457] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:39,470] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:39,470] [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_007992495.1	s__Reyranella soli	100.0	3075	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016185145.1	s__Reyranella sp016185145	89.7859	1855	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	89.3916	2010	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	88.9705	2079	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825855.1	s__Reyranella sp902825855	88.7788	1767	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	88.4411	1684	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780605.1	s__Reyranella sp016780605	86.3684	925	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870055.1	s__Reyranella sp016870055	84.2527	1090	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	83.6844	957	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	82.9032	1112	3090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191435.1	s__JACPOQ01 sp016191435	78.3123	117	3090	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACPOQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:39,473] [INFO] GTDB search result was written to GCF_007992495.1_ASM799249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:39,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:39,479] [INFO] DFAST_QC result json was written to GCF_007992495.1_ASM799249v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:39,480] [INFO] DFAST_QC completed!
[2024-01-24 14:41:39,480] [INFO] Total running time: 0h2m39s