[2024-01-24 15:27:21,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg04a30ad3-736d-424c-868e-beb3e89f90fa/dqc_reference
[2024-01-24 15:27:22,979] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:22,980] [INFO] Task started: Prodigal
[2024-01-24 15:27:22,980] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6982dfa-4486-4f39-913a-dd59d61fb836/GCF_003065485.1_ASM306548v1_genomic.fna.gz | prodigal -d GCF_003065485.1_ASM306548v1_genomic.fna/cds.fna -a GCF_003065485.1_ASM306548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:32,033] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:32,034] [INFO] Task started: HMMsearch
[2024-01-24 15:27:32,034] [INFO] Running command: hmmsearch --tblout GCF_003065485.1_ASM306548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04a30ad3-736d-424c-868e-beb3e89f90fa/dqc_reference/reference_markers.hmm GCF_003065485.1_ASM306548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:32,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:32,298] [INFO] Found 6/6 markers.
[2024-01-24 15:27:32,327] [INFO] Query marker FASTA was written to GCF_003065485.1_ASM306548v1_genomic.fna/markers.fasta
[2024-01-24 15:27:32,327] [INFO] Task started: Blastn
[2024-01-24 15:27:32,328] [INFO] Running command: blastn -query GCF_003065485.1_ASM306548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04a30ad3-736d-424c-868e-beb3e89f90fa/dqc_reference/reference_markers.fasta -out GCF_003065485.1_ASM306548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:33,355] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:33,359] [INFO] Selected 32 target genomes.
[2024-01-24 15:27:33,359] [INFO] Target genome list was writen to GCF_003065485.1_ASM306548v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:33,368] [INFO] Task started: fastANI
[2024-01-24 15:27:33,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6982dfa-4486-4f39-913a-dd59d61fb836/GCF_003065485.1_ASM306548v1_genomic.fna.gz --refList GCF_003065485.1_ASM306548v1_genomic.fna/target_genomes.txt --output GCF_003065485.1_ASM306548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:51,391] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:51,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04a30ad3-736d-424c-868e-beb3e89f90fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:51,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04a30ad3-736d-424c-868e-beb3e89f90fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:51,418] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:51,418] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:51,418] [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
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.7545	203	936	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.6955	247	936	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	78.5934	223	936	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	78.5763	266	936	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.5695	207	936	95	below_threshold
Marisediminicola antarctica	strain=ZS314	GCA_009930795.1	674079	674079	type	True	78.5538	232	936	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.4959	197	936	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	78.4747	202	936	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	78.441	210	936	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	78.4308	189	936	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.3967	244	936	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.3606	206	936	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	78.3589	190	936	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.3316	195	936	95	below_threshold
Subtercola boreus	strain=K300	GCA_003399685.1	120213	120213	suspected-type	True	78.2921	186	936	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	78.286	218	936	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.2189	208	936	95	below_threshold
Salinibacterium amurskyense	strain=JCM 12362	GCA_003668745.1	205941	205941	type	True	78.1856	164	936	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	78.1544	210	936	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.136	199	936	95	below_threshold
Salinibacterium amurskyense	strain=DSM 16400	GCA_002797685.1	205941	205941	type	True	78.1188	159	936	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.0632	242	936	95	below_threshold
Plantibacter flavus	strain=DSM 14012	GCA_003755125.1	150123	150123	type	True	78.0261	197	936	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.9885	217	936	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.8885	215	936	95	below_threshold
Plantibacter flavus	strain=VKM Ac-2504	GCA_900177615.1	150123	150123	type	True	77.862	193	936	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	77.8098	155	936	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	77.736	211	936	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.5328	169	936	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	77.4693	99	936	95	below_threshold
Spelaeicoccus albus	strain=DSM 26341	GCA_013409065.1	1280376	1280376	type	True	76.6992	50	936	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	76.4152	91	936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:51,420] [INFO] DFAST Taxonomy check result was written to GCF_003065485.1_ASM306548v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:51,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:51,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:51,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04a30ad3-736d-424c-868e-beb3e89f90fa/dqc_reference/checkm_data
[2024-01-24 15:27:51,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:51,449] [INFO] Task started: CheckM
[2024-01-24 15:27:51,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003065485.1_ASM306548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003065485.1_ASM306548v1_genomic.fna/checkm_input GCF_003065485.1_ASM306548v1_genomic.fna/checkm_result
[2024-01-24 15:28:21,352] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:21,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:21,375] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:21,376] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:21,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003065485.1_ASM306548v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:21,376] [INFO] Task started: Blastn
[2024-01-24 15:28:21,377] [INFO] Running command: blastn -query GCF_003065485.1_ASM306548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04a30ad3-736d-424c-868e-beb3e89f90fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003065485.1_ASM306548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:22,789] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:22,793] [INFO] Selected 17 target genomes.
[2024-01-24 15:28:22,794] [INFO] Target genome list was writen to GCF_003065485.1_ASM306548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:22,810] [INFO] Task started: fastANI
[2024-01-24 15:28:22,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6982dfa-4486-4f39-913a-dd59d61fb836/GCF_003065485.1_ASM306548v1_genomic.fna.gz --refList GCF_003065485.1_ASM306548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003065485.1_ASM306548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:32,501] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:32,518] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:32,519] [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_003065485.1	s__Homoserinimonas hongtaonis	100.0	935	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	98.79	98.79	0.93	0.93	2	conclusive
GCF_008001035.1	s__Homoserinimonas sp008001035	79.8787	416	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015234465.1	s__Homoserinimonas sp015234465	79.7808	405	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716125.1	s__Homoserinimonas aerilata	79.6726	356	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755725.1	s__ZJ450 sp009755725	78.7254	204	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__ZJ450	95.0	98.36	98.36	0.94	0.94	2	-
GCF_011057645.1	s__Marisediminicola senii	78.412	243	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012274275.1	s__Terrimesophilobacter sp012274275	78.4064	211	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Terrimesophilobacter	95.0	98.97	98.97	0.95	0.95	2	-
GCA_002280615.1	s__Chryseoglobus sp002280615	78.3803	131	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402215.1	s__Cryobacterium sp004402215	78.3357	199	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502775.1	s__Herbiconiux sp005502775	78.2443	207	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	99.99	99.99	0.97	0.97	2	-
GCF_014217685.1	s__Lacisediminihabitans sp014217685	78.2288	225	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355965.1	s__JAFIQW01 sp017355965	78.1976	223	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929555.1	s__Cryobacterium sp002929555	78.1919	206	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834185.1	s__Rathayibacter sp009834185	78.145	209	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205055.1	s__Rathayibacter sp013205055	78.1087	199	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177765.1	s__Agreia sp900177765	78.0966	184	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agreia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003454135.1	s__Lacisediminihabitans sp003454135	77.7192	179	936	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:32,522] [INFO] GTDB search result was written to GCF_003065485.1_ASM306548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:32,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:32,528] [INFO] DFAST_QC result json was written to GCF_003065485.1_ASM306548v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:32,528] [INFO] DFAST_QC completed!
[2024-01-24 15:28:32,528] [INFO] Total running time: 0h1m11s