[2023-06-29 15:09:43,016] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:09:43,019] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:09:43,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg04e0cf95-369f-4012-be4a-f1087fec1415/dqc_reference
[2023-06-29 15:09:44,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:09:44,206] [INFO] Task started: Prodigal
[2023-06-29 15:09:44,207] [INFO] Running command: gunzip -c /var/lib/cwl/stg72dcc011-2205-4f4f-b42b-f94b8bbfff84/GCA_021785515.1_ASM2178551v1_genomic.fna.gz | prodigal -d GCA_021785515.1_ASM2178551v1_genomic.fna/cds.fna -a GCA_021785515.1_ASM2178551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:09:53,326] [INFO] Task succeeded: Prodigal
[2023-06-29 15:09:53,327] [INFO] Task started: HMMsearch
[2023-06-29 15:09:53,327] [INFO] Running command: hmmsearch --tblout GCA_021785515.1_ASM2178551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04e0cf95-369f-4012-be4a-f1087fec1415/dqc_reference/reference_markers.hmm GCA_021785515.1_ASM2178551v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:09:53,538] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:09:53,539] [INFO] Found 6/6 markers.
[2023-06-29 15:09:53,566] [INFO] Query marker FASTA was written to GCA_021785515.1_ASM2178551v1_genomic.fna/markers.fasta
[2023-06-29 15:09:53,567] [INFO] Task started: Blastn
[2023-06-29 15:09:53,567] [INFO] Running command: blastn -query GCA_021785515.1_ASM2178551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04e0cf95-369f-4012-be4a-f1087fec1415/dqc_reference/reference_markers.fasta -out GCA_021785515.1_ASM2178551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:09:54,193] [INFO] Task succeeded: Blastn
[2023-06-29 15:09:54,206] [INFO] Selected 28 target genomes.
[2023-06-29 15:09:54,207] [INFO] Target genome list was writen to GCA_021785515.1_ASM2178551v1_genomic.fna/target_genomes.txt
[2023-06-29 15:09:54,210] [INFO] Task started: fastANI
[2023-06-29 15:09:54,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg72dcc011-2205-4f4f-b42b-f94b8bbfff84/GCA_021785515.1_ASM2178551v1_genomic.fna.gz --refList GCA_021785515.1_ASM2178551v1_genomic.fna/target_genomes.txt --output GCA_021785515.1_ASM2178551v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:10:10,748] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:10,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04e0cf95-369f-4012-be4a-f1087fec1415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:10:10,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04e0cf95-369f-4012-be4a-f1087fec1415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:10:10,760] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:10:10,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:10:10,761] [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
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	76.8246	103	1008	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.4232	74	1008	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	76.3996	102	1008	95	below_threshold
Acidiferrobacter thiooxydans	strain=m-1	GCA_003333315.1	163359	163359	type	True	76.3835	59	1008	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.3507	53	1008	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.3198	71	1008	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.122	55	1008	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.9007	64	1008	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	75.8615	50	1008	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.8047	76	1008	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.7453	56	1008	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.6179	55	1008	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.6155	57	1008	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.1864	51	1008	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:10:10,762] [INFO] DFAST Taxonomy check result was written to GCA_021785515.1_ASM2178551v1_genomic.fna/tc_result.tsv
[2023-06-29 15:10:10,763] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:10:10,763] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:10:10,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04e0cf95-369f-4012-be4a-f1087fec1415/dqc_reference/checkm_data
[2023-06-29 15:10:10,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:10:10,794] [INFO] Task started: CheckM
[2023-06-29 15:10:10,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021785515.1_ASM2178551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021785515.1_ASM2178551v1_genomic.fna/checkm_input GCA_021785515.1_ASM2178551v1_genomic.fna/checkm_result
[2023-06-29 15:10:40,830] [INFO] Task succeeded: CheckM
[2023-06-29 15:10:40,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:10:40,850] [INFO] ===== Completeness check finished =====
[2023-06-29 15:10:40,850] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:10:40,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021785515.1_ASM2178551v1_genomic.fna/markers.fasta)
[2023-06-29 15:10:40,851] [INFO] Task started: Blastn
[2023-06-29 15:10:40,851] [INFO] Running command: blastn -query GCA_021785515.1_ASM2178551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04e0cf95-369f-4012-be4a-f1087fec1415/dqc_reference/reference_markers_gtdb.fasta -out GCA_021785515.1_ASM2178551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:10:41,852] [INFO] Task succeeded: Blastn
[2023-06-29 15:10:41,856] [INFO] Selected 27 target genomes.
[2023-06-29 15:10:41,856] [INFO] Target genome list was writen to GCA_021785515.1_ASM2178551v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:10:41,871] [INFO] Task started: fastANI
[2023-06-29 15:10:41,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg72dcc011-2205-4f4f-b42b-f94b8bbfff84/GCA_021785515.1_ASM2178551v1_genomic.fna.gz --refList GCA_021785515.1_ASM2178551v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021785515.1_ASM2178551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:10:55,818] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:55,829] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:10:55,829] [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_016218345.1	s__JACREH01 sp016218345	76.8257	99	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__UBA6901;g__JACREH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355735.1	s__Sulfuricaulis limicola	76.8019	104	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001785175.1	s__MFSY01 sp001785175	76.6032	80	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__MFSY01	95.0	97.98	97.98	0.76	0.76	2	-
GCF_003337735.1	s__Thioalbus denitrificans	76.4232	74	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355415.1	s__Sulfurifustis variabilis	76.3996	102	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfurifustis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333315.1	s__Acidiferrobacter thiooxydans	76.3835	59	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Acidiferrobacteraceae;g__Acidiferrobacter	95.0	99.34	99.34	0.91	0.91	2	-
GCA_001304215.1	s__SM1-46 sp001304215	76.3595	55	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__SM1-46	95.0	96.54	95.14	0.75	0.71	4	-
GCA_004298065.1	s__SCRL01 sp004298065	76.3467	97	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__SCRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	76.3444	70	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001785115.1	s__RBG-16-65-34 sp001785115	76.0464	65	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__RBG-16-65-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695825.1	s__J048 sp003695825	75.4811	52	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:10:55,831] [INFO] GTDB search result was written to GCA_021785515.1_ASM2178551v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:10:55,832] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:10:55,836] [INFO] DFAST_QC result json was written to GCA_021785515.1_ASM2178551v1_genomic.fna/dqc_result.json
[2023-06-29 15:10:55,836] [INFO] DFAST_QC completed!
[2023-06-29 15:10:55,836] [INFO] Total running time: 0h1m13s