[2023-06-26 21:37:11,796] [INFO] DFAST_QC pipeline started.
[2023-06-26 21:37:11,799] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 21:37:11,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgb79aa82d-5a09-4382-9ad4-a37240bde8a8/dqc_reference
[2023-06-26 21:37:13,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 21:37:13,089] [INFO] Task started: Prodigal
[2023-06-26 21:37:13,090] [INFO] Running command: gunzip -c /var/lib/cwl/stga99f9d59-4a73-4b03-950a-4b5829607362/GCA_027321585.1_ASM2732158v1_genomic.fna.gz | prodigal -d GCA_027321585.1_ASM2732158v1_genomic.fna/cds.fna -a GCA_027321585.1_ASM2732158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 21:37:19,751] [INFO] Task succeeded: Prodigal
[2023-06-26 21:37:19,752] [INFO] Task started: HMMsearch
[2023-06-26 21:37:19,752] [INFO] Running command: hmmsearch --tblout GCA_027321585.1_ASM2732158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb79aa82d-5a09-4382-9ad4-a37240bde8a8/dqc_reference/reference_markers.hmm GCA_027321585.1_ASM2732158v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 21:37:20,008] [INFO] Task succeeded: HMMsearch
[2023-06-26 21:37:20,011] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga99f9d59-4a73-4b03-950a-4b5829607362/GCA_027321585.1_ASM2732158v1_genomic.fna.gz]
[2023-06-26 21:37:20,050] [INFO] Query marker FASTA was written to GCA_027321585.1_ASM2732158v1_genomic.fna/markers.fasta
[2023-06-26 21:37:20,051] [INFO] Task started: Blastn
[2023-06-26 21:37:20,051] [INFO] Running command: blastn -query GCA_027321585.1_ASM2732158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb79aa82d-5a09-4382-9ad4-a37240bde8a8/dqc_reference/reference_markers.fasta -out GCA_027321585.1_ASM2732158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:37:20,998] [INFO] Task succeeded: Blastn
[2023-06-26 21:37:21,004] [INFO] Selected 19 target genomes.
[2023-06-26 21:37:21,004] [INFO] Target genome list was writen to GCA_027321585.1_ASM2732158v1_genomic.fna/target_genomes.txt
[2023-06-26 21:37:21,009] [INFO] Task started: fastANI
[2023-06-26 21:37:21,009] [INFO] Running command: fastANI --query /var/lib/cwl/stga99f9d59-4a73-4b03-950a-4b5829607362/GCA_027321585.1_ASM2732158v1_genomic.fna.gz --refList GCA_027321585.1_ASM2732158v1_genomic.fna/target_genomes.txt --output GCA_027321585.1_ASM2732158v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 21:37:32,802] [INFO] Task succeeded: fastANI
[2023-06-26 21:37:32,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb79aa82d-5a09-4382-9ad4-a37240bde8a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 21:37:32,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb79aa82d-5a09-4382-9ad4-a37240bde8a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 21:37:32,830] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 21:37:32,830] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 21:37:32,832] [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=J1A	GCA_003967275.1	1914471	1914471	type	True	77.7102	188	685	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	77.7082	181	685	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.6661	187	685	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	77.5138	186	685	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.2989	135	685	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	76.9324	116	685	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	76.8867	117	685	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.6259	82	685	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	76.5126	102	685	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	76.443	111	685	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.1909	127	685	95	below_threshold
Immundisolibacter cernigliae	strain=TR3.2	GCA_001697225.1	1810504	1810504	type	True	76.115	76	685	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	76.0696	70	685	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	75.8925	52	685	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	75.8302	62	685	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.7295	65	685	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.6588	64	685	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 21:37:32,836] [INFO] DFAST Taxonomy check result was written to GCA_027321585.1_ASM2732158v1_genomic.fna/tc_result.tsv
[2023-06-26 21:37:32,837] [INFO] ===== Taxonomy check completed =====
[2023-06-26 21:37:32,837] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 21:37:32,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb79aa82d-5a09-4382-9ad4-a37240bde8a8/dqc_reference/checkm_data
[2023-06-26 21:37:32,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 21:37:32,873] [INFO] Task started: CheckM
[2023-06-26 21:37:32,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027321585.1_ASM2732158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027321585.1_ASM2732158v1_genomic.fna/checkm_input GCA_027321585.1_ASM2732158v1_genomic.fna/checkm_result
[2023-06-26 21:37:59,534] [INFO] Task succeeded: CheckM
[2023-06-26 21:37:59,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-26 21:37:59,564] [INFO] ===== Completeness check finished =====
[2023-06-26 21:37:59,565] [INFO] ===== Start GTDB Search =====
[2023-06-26 21:37:59,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027321585.1_ASM2732158v1_genomic.fna/markers.fasta)
[2023-06-26 21:37:59,566] [INFO] Task started: Blastn
[2023-06-26 21:37:59,566] [INFO] Running command: blastn -query GCA_027321585.1_ASM2732158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb79aa82d-5a09-4382-9ad4-a37240bde8a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_027321585.1_ASM2732158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:38:01,225] [INFO] Task succeeded: Blastn
[2023-06-26 21:38:01,231] [INFO] Selected 17 target genomes.
[2023-06-26 21:38:01,231] [INFO] Target genome list was writen to GCA_027321585.1_ASM2732158v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 21:38:01,246] [INFO] Task started: fastANI
[2023-06-26 21:38:01,246] [INFO] Running command: fastANI --query /var/lib/cwl/stga99f9d59-4a73-4b03-950a-4b5829607362/GCA_027321585.1_ASM2732158v1_genomic.fna.gz --refList GCA_027321585.1_ASM2732158v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027321585.1_ASM2732158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 21:38:10,685] [INFO] Task succeeded: fastANI
[2023-06-26 21:38:10,707] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 21:38:10,707] [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_008923285.1	s__UBA6918 sp008923285	78.7304	208	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA6918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421825.1	s__UBA6918 sp002421825	78.1078	188	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA6918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820765.1	s__Thiobacillus sp018820765	78.0541	220	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCA_016195805.1	s__Thiobacillus sp016195805	77.9135	203	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327405.1	s__UBA6918 sp002327405	77.7043	160	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA6918	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001530125.1	s__Thiobacillus denitrificans_C	77.6106	184	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	77.6093	204	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_001899305.1	s__Thiobacillus sp001899305	77.5753	194	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.65	95.89	0.93	0.87	5	-
GCA_016124745.1	s__Thiobacillus sp016124745	77.5293	162	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897675.1	s__Thiobacillus sp001897675	77.5243	184	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	95.41	95.18	0.77	0.76	3	-
GCF_000376425.1	s__Thiobacillus denitrificans	77.5138	186	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780105.1	s__Thiobacillus sp018780105	77.4881	178	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008923315.1	s__Thiobacillus sp001897705	77.4699	187	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	98.92	98.92	0.91	0.90	4	-
GCA_018262815.1	s__Thiobacillus sp018262815	77.3644	148	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424845.1	s__Thiobacillus denitrificans_F	77.0515	122	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263115.1	s__JACAED01 sp018263115	76.7239	136	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__JACAED01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780025.1	s__Thiobacillus sp018780025	76.4065	66	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 21:38:10,712] [INFO] GTDB search result was written to GCA_027321585.1_ASM2732158v1_genomic.fna/result_gtdb.tsv
[2023-06-26 21:38:10,714] [INFO] ===== GTDB Search completed =====
[2023-06-26 21:38:10,726] [INFO] DFAST_QC result json was written to GCA_027321585.1_ASM2732158v1_genomic.fna/dqc_result.json
[2023-06-26 21:38:10,726] [INFO] DFAST_QC completed!
[2023-06-26 21:38:10,726] [INFO] Total running time: 0h0m59s