[2023-07-01 07:01:45,175] [INFO] DFAST_QC pipeline started.
[2023-07-01 07:01:45,179] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 07:01:45,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg99b7bc71-097a-4b67-9630-2043526f9f73/dqc_reference
[2023-07-01 07:01:46,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 07:01:46,949] [INFO] Task started: Prodigal
[2023-07-01 07:01:46,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg25238905-3acd-4cae-b10e-9491f4614a35/GCA_008080525.1_ASM808052v1_genomic.fna.gz | prodigal -d GCA_008080525.1_ASM808052v1_genomic.fna/cds.fna -a GCA_008080525.1_ASM808052v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 07:01:55,127] [INFO] Task succeeded: Prodigal
[2023-07-01 07:01:55,128] [INFO] Task started: HMMsearch
[2023-07-01 07:01:55,128] [INFO] Running command: hmmsearch --tblout GCA_008080525.1_ASM808052v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99b7bc71-097a-4b67-9630-2043526f9f73/dqc_reference/reference_markers.hmm GCA_008080525.1_ASM808052v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 07:01:55,352] [INFO] Task succeeded: HMMsearch
[2023-07-01 07:01:55,353] [INFO] Found 6/6 markers.
[2023-07-01 07:01:55,380] [INFO] Query marker FASTA was written to GCA_008080525.1_ASM808052v1_genomic.fna/markers.fasta
[2023-07-01 07:01:55,380] [INFO] Task started: Blastn
[2023-07-01 07:01:55,380] [INFO] Running command: blastn -query GCA_008080525.1_ASM808052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99b7bc71-097a-4b67-9630-2043526f9f73/dqc_reference/reference_markers.fasta -out GCA_008080525.1_ASM808052v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:01:56,191] [INFO] Task succeeded: Blastn
[2023-07-01 07:01:56,194] [INFO] Selected 21 target genomes.
[2023-07-01 07:01:56,195] [INFO] Target genome list was writen to GCA_008080525.1_ASM808052v1_genomic.fna/target_genomes.txt
[2023-07-01 07:01:56,195] [INFO] Task started: fastANI
[2023-07-01 07:01:56,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg25238905-3acd-4cae-b10e-9491f4614a35/GCA_008080525.1_ASM808052v1_genomic.fna.gz --refList GCA_008080525.1_ASM808052v1_genomic.fna/target_genomes.txt --output GCA_008080525.1_ASM808052v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 07:02:09,886] [INFO] Task succeeded: fastANI
[2023-07-01 07:02:09,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99b7bc71-097a-4b67-9630-2043526f9f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 07:02:09,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99b7bc71-097a-4b67-9630-2043526f9f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 07:02:09,909] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 07:02:09,909] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 07:02:09,910] [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
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	80.4737	382	896	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	80.466	385	896	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.3911	289	896	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	78.0569	268	896	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.012	257	896	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	77.7123	212	896	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.6516	184	896	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	77.6507	216	896	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.6213	219	896	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	77.3731	226	896	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.2308	167	896	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	77.2103	161	896	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	77.1904	274	896	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.1517	163	896	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.8704	158	896	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	76.8305	192	896	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	76.7803	159	896	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.6934	201	896	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.6441	147	896	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.2485	146	896	95	below_threshold
Stenotrophomonas ginsengisoli	strain=DSM 24757	GCA_001431485.1	336566	336566	type	True	76.2294	91	896	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 07:02:09,913] [INFO] DFAST Taxonomy check result was written to GCA_008080525.1_ASM808052v1_genomic.fna/tc_result.tsv
[2023-07-01 07:02:09,914] [INFO] ===== Taxonomy check completed =====
[2023-07-01 07:02:09,915] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 07:02:09,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99b7bc71-097a-4b67-9630-2043526f9f73/dqc_reference/checkm_data
[2023-07-01 07:02:09,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 07:02:09,951] [INFO] Task started: CheckM
[2023-07-01 07:02:09,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008080525.1_ASM808052v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008080525.1_ASM808052v1_genomic.fna/checkm_input GCA_008080525.1_ASM808052v1_genomic.fna/checkm_result
[2023-07-01 07:02:37,827] [INFO] Task succeeded: CheckM
[2023-07-01 07:02:37,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 07:02:37,844] [INFO] ===== Completeness check finished =====
[2023-07-01 07:02:37,844] [INFO] ===== Start GTDB Search =====
[2023-07-01 07:02:37,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008080525.1_ASM808052v1_genomic.fna/markers.fasta)
[2023-07-01 07:02:37,845] [INFO] Task started: Blastn
[2023-07-01 07:02:37,845] [INFO] Running command: blastn -query GCA_008080525.1_ASM808052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99b7bc71-097a-4b67-9630-2043526f9f73/dqc_reference/reference_markers_gtdb.fasta -out GCA_008080525.1_ASM808052v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:02:39,301] [INFO] Task succeeded: Blastn
[2023-07-01 07:02:39,305] [INFO] Selected 10 target genomes.
[2023-07-01 07:02:39,305] [INFO] Target genome list was writen to GCA_008080525.1_ASM808052v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 07:02:39,306] [INFO] Task started: fastANI
[2023-07-01 07:02:39,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg25238905-3acd-4cae-b10e-9491f4614a35/GCA_008080525.1_ASM808052v1_genomic.fna.gz --refList GCA_008080525.1_ASM808052v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008080525.1_ASM808052v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 07:02:46,469] [INFO] Task succeeded: fastANI
[2023-07-01 07:02:46,478] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 07:02:46,478] [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
GCA_009772925.1	s__PFJX01 sp009772925	99.9755	894	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.99	99.98	1.00	0.99	4	conclusive
GCA_016873935.1	s__PFJX01 sp016873935	93.8496	656	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719465.1	s__PFJX01 sp016719465	85.1267	620	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.31	99.27	0.95	0.94	3	-
GCA_016219425.1	s__PFJX01 sp016219425	81.6647	456	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360535.1	s__UBA3361 sp002360535	80.8727	453	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA3361	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013335435.1	s__Parasulfuritortus sp013335435	80.7448	375	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337445.1	s__Parasulfuritortus cantonensis	80.5511	374	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784045.1	s__PFJX01 sp002784045	79.9786	401	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.74	99.63	0.93	0.93	3	-
GCA_002281555.1	s__PFJX01 sp002281555	79.6744	431	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903835655.1	s__PFJX01 sp903835655	79.5282	397	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.87	99.69	0.96	0.90	25	-
--------------------------------------------------------------------------------
[2023-07-01 07:02:46,502] [INFO] GTDB search result was written to GCA_008080525.1_ASM808052v1_genomic.fna/result_gtdb.tsv
[2023-07-01 07:02:46,502] [INFO] ===== GTDB Search completed =====
[2023-07-01 07:02:46,506] [INFO] DFAST_QC result json was written to GCA_008080525.1_ASM808052v1_genomic.fna/dqc_result.json
[2023-07-01 07:02:46,506] [INFO] DFAST_QC completed!
[2023-07-01 07:02:46,506] [INFO] Total running time: 0h1m1s