[2024-01-24 13:18:45,993] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg13e30507-ecd4-4413-ad7d-1e50484a903f/dqc_reference
[2024-01-24 13:18:47,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,265] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,265] [INFO] Running command: gunzip -c /var/lib/cwl/stg54b81c8b-b64b-4ed6-a8c6-e6f9521f1b15/GCF_016806835.2_ASM1680683v2_genomic.fna.gz | prodigal -d GCF_016806835.2_ASM1680683v2_genomic.fna/cds.fna -a GCF_016806835.2_ASM1680683v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:10,341] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:10,342] [INFO] Task started: HMMsearch
[2024-01-24 13:19:10,342] [INFO] Running command: hmmsearch --tblout GCF_016806835.2_ASM1680683v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13e30507-ecd4-4413-ad7d-1e50484a903f/dqc_reference/reference_markers.hmm GCF_016806835.2_ASM1680683v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:10,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:10,704] [INFO] Found 6/6 markers.
[2024-01-24 13:19:10,764] [INFO] Query marker FASTA was written to GCF_016806835.2_ASM1680683v2_genomic.fna/markers.fasta
[2024-01-24 13:19:10,765] [INFO] Task started: Blastn
[2024-01-24 13:19:10,765] [INFO] Running command: blastn -query GCF_016806835.2_ASM1680683v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e30507-ecd4-4413-ad7d-1e50484a903f/dqc_reference/reference_markers.fasta -out GCF_016806835.2_ASM1680683v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:11,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:11,646] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:11,647] [INFO] Target genome list was writen to GCF_016806835.2_ASM1680683v2_genomic.fna/target_genomes.txt
[2024-01-24 13:19:11,652] [INFO] Task started: fastANI
[2024-01-24 13:19:11,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg54b81c8b-b64b-4ed6-a8c6-e6f9521f1b15/GCF_016806835.2_ASM1680683v2_genomic.fna.gz --refList GCF_016806835.2_ASM1680683v2_genomic.fna/target_genomes.txt --output GCF_016806835.2_ASM1680683v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:33,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:33,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13e30507-ecd4-4413-ad7d-1e50484a903f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:33,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13e30507-ecd4-4413-ad7d-1e50484a903f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:33,897] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:33,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:33,898] [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 rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	100.0	2580	2582	95	conclusive
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	93.1809	2175	2582	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	92.111	1769	2582	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	84.3889	1614	2582	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	82.7838	1562	2582	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	79.186	702	2582	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	79.0275	851	2582	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	78.8616	786	2582	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	78.8512	840	2582	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	78.5827	751	2582	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.5339	748	2582	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	77.953	576	2582	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.7259	359	2582	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,899] [INFO] DFAST Taxonomy check result was written to GCF_016806835.2_ASM1680683v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:33,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:33,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:33,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13e30507-ecd4-4413-ad7d-1e50484a903f/dqc_reference/checkm_data
[2024-01-24 13:19:33,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:33,976] [INFO] Task started: CheckM
[2024-01-24 13:19:33,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016806835.2_ASM1680683v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016806835.2_ASM1680683v2_genomic.fna/checkm_input GCF_016806835.2_ASM1680683v2_genomic.fna/checkm_result
[2024-01-24 13:20:38,883] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:38,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:38,902] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:38,902] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:38,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016806835.2_ASM1680683v2_genomic.fna/markers.fasta)
[2024-01-24 13:20:38,902] [INFO] Task started: Blastn
[2024-01-24 13:20:38,903] [INFO] Running command: blastn -query GCF_016806835.2_ASM1680683v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e30507-ecd4-4413-ad7d-1e50484a903f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016806835.2_ASM1680683v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:40,491] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:40,494] [INFO] Selected 6 target genomes.
[2024-01-24 13:20:40,494] [INFO] Target genome list was writen to GCF_016806835.2_ASM1680683v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:40,525] [INFO] Task started: fastANI
[2024-01-24 13:20:40,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg54b81c8b-b64b-4ed6-a8c6-e6f9521f1b15/GCF_016806835.2_ASM1680683v2_genomic.fna.gz --refList GCF_016806835.2_ASM1680683v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016806835.2_ASM1680683v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:53,215] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:53,221] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:53,221] [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_016806835.1	s__Skermanella rosea	99.9692	2493	2582	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_016653635.2	s__Skermanella sp016653635	94.5811	2084	2582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	93.1507	2116	2582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	92.1351	1767	2582	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	84.3993	1611	2582	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	82.7666	1566	2582	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 13:20:53,223] [INFO] GTDB search result was written to GCF_016806835.2_ASM1680683v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:53,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:53,226] [INFO] DFAST_QC result json was written to GCF_016806835.2_ASM1680683v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:53,226] [INFO] DFAST_QC completed!
[2024-01-24 13:20:53,226] [INFO] Total running time: 0h2m7s