[2024-01-24 10:57:37,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:37,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:37,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c81b0db-b438-41b8-a10b-f4a8a8c1c591/dqc_reference
[2024-01-24 10:57:39,369] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,371] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,372] [INFO] Running command: gunzip -c /var/lib/cwl/stgf59cc056-1315-44c1-aceb-82c4a56fa958/GCF_016765655.2_ASM1676565v2_genomic.fna.gz | prodigal -d GCF_016765655.2_ASM1676565v2_genomic.fna/cds.fna -a GCF_016765655.2_ASM1676565v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:04,208] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:04,209] [INFO] Task started: HMMsearch
[2024-01-24 10:58:04,209] [INFO] Running command: hmmsearch --tblout GCF_016765655.2_ASM1676565v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c81b0db-b438-41b8-a10b-f4a8a8c1c591/dqc_reference/reference_markers.hmm GCF_016765655.2_ASM1676565v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:04,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:04,581] [INFO] Found 6/6 markers.
[2024-01-24 10:58:04,646] [INFO] Query marker FASTA was written to GCF_016765655.2_ASM1676565v2_genomic.fna/markers.fasta
[2024-01-24 10:58:04,647] [INFO] Task started: Blastn
[2024-01-24 10:58:04,647] [INFO] Running command: blastn -query GCF_016765655.2_ASM1676565v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c81b0db-b438-41b8-a10b-f4a8a8c1c591/dqc_reference/reference_markers.fasta -out GCF_016765655.2_ASM1676565v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:05,772] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:05,778] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:05,779] [INFO] Target genome list was writen to GCF_016765655.2_ASM1676565v2_genomic.fna/target_genomes.txt
[2024-01-24 10:58:05,822] [INFO] Task started: fastANI
[2024-01-24 10:58:05,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59cc056-1315-44c1-aceb-82c4a56fa958/GCF_016765655.2_ASM1676565v2_genomic.fna.gz --refList GCF_016765655.2_ASM1676565v2_genomic.fna/target_genomes.txt --output GCF_016765655.2_ASM1676565v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:23,179] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:23,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c81b0db-b438-41b8-a10b-f4a8a8c1c591/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:23,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c81b0db-b438-41b8-a10b-f4a8a8c1c591/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:23,192] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:23,193] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:23,193] [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	100.0	2606	2610	95	conclusive
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	93.2682	1756	2610	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	93.0933	2184	2610	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	84.2098	1630	2610	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	82.7292	1553	2610	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	78.9402	818	2610	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	78.8553	751	2610	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.3052	748	2610	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	77.8311	567	2610	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.8238	290	2610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,196] [INFO] DFAST Taxonomy check result was written to GCF_016765655.2_ASM1676565v2_genomic.fna/tc_result.tsv
[2024-01-24 10:58:23,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:23,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:23,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c81b0db-b438-41b8-a10b-f4a8a8c1c591/dqc_reference/checkm_data
[2024-01-24 10:58:23,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:23,275] [INFO] Task started: CheckM
[2024-01-24 10:58:23,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016765655.2_ASM1676565v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016765655.2_ASM1676565v2_genomic.fna/checkm_input GCF_016765655.2_ASM1676565v2_genomic.fna/checkm_result
[2024-01-24 10:59:33,909] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:33,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:33,939] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:33,939] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:33,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016765655.2_ASM1676565v2_genomic.fna/markers.fasta)
[2024-01-24 10:59:33,940] [INFO] Task started: Blastn
[2024-01-24 10:59:33,940] [INFO] Running command: blastn -query GCF_016765655.2_ASM1676565v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c81b0db-b438-41b8-a10b-f4a8a8c1c591/dqc_reference/reference_markers_gtdb.fasta -out GCF_016765655.2_ASM1676565v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:35,874] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:35,878] [INFO] Selected 6 target genomes.
[2024-01-24 10:59:35,878] [INFO] Target genome list was writen to GCF_016765655.2_ASM1676565v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:35,884] [INFO] Task started: fastANI
[2024-01-24 10:59:35,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59cc056-1315-44c1-aceb-82c4a56fa958/GCF_016765655.2_ASM1676565v2_genomic.fna.gz --refList GCF_016765655.2_ASM1676565v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016765655.2_ASM1676565v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:49,965] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:49,977] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:49,978] [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_016765655.1	s__Skermanella mucosa	99.944	2475	2610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008843145.1	s__Skermanella pratensis	93.2745	1754	2610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806835.1	s__Skermanella rosea	93.1087	2149	2610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	92.2694	2054	2610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576635.1	s__Skermanella stibiiresistens	84.187	1635	2610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000936425.1	s__Skermanella aerolata	82.7375	1550	2610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:49,979] [INFO] GTDB search result was written to GCF_016765655.2_ASM1676565v2_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:49,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:49,983] [INFO] DFAST_QC result json was written to GCF_016765655.2_ASM1676565v2_genomic.fna/dqc_result.json
[2024-01-24 10:59:49,983] [INFO] DFAST_QC completed!
[2024-01-24 10:59:49,983] [INFO] Total running time: 0h2m12s