[2024-01-24 13:49:41,063] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:41,064] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:41,064] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe36141e-8912-4edf-b011-2c6ef97b11aa/dqc_reference
[2024-01-24 13:49:42,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,443] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg11d17175-26f7-4052-88f4-33b5e9c827c0/GCF_017901135.1_ASM1790113v1_genomic.fna.gz | prodigal -d GCF_017901135.1_ASM1790113v1_genomic.fna/cds.fna -a GCF_017901135.1_ASM1790113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:58,507] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:58,507] [INFO] Task started: HMMsearch
[2024-01-24 13:49:58,507] [INFO] Running command: hmmsearch --tblout GCF_017901135.1_ASM1790113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe36141e-8912-4edf-b011-2c6ef97b11aa/dqc_reference/reference_markers.hmm GCF_017901135.1_ASM1790113v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:58,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:58,794] [INFO] Found 6/6 markers.
[2024-01-24 13:49:58,840] [INFO] Query marker FASTA was written to GCF_017901135.1_ASM1790113v1_genomic.fna/markers.fasta
[2024-01-24 13:49:58,840] [INFO] Task started: Blastn
[2024-01-24 13:49:58,840] [INFO] Running command: blastn -query GCF_017901135.1_ASM1790113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe36141e-8912-4edf-b011-2c6ef97b11aa/dqc_reference/reference_markers.fasta -out GCF_017901135.1_ASM1790113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:59,650] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:59,654] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:59,655] [INFO] Target genome list was writen to GCF_017901135.1_ASM1790113v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:59,659] [INFO] Task started: fastANI
[2024-01-24 13:49:59,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d17175-26f7-4052-88f4-33b5e9c827c0/GCF_017901135.1_ASM1790113v1_genomic.fna.gz --refList GCF_017901135.1_ASM1790113v1_genomic.fna/target_genomes.txt --output GCF_017901135.1_ASM1790113v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:11,183] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:11,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe36141e-8912-4edf-b011-2c6ef97b11aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:11,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe36141e-8912-4edf-b011-2c6ef97b11aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:11,194] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:11,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:11,195] [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
Thiothrix litoralis	strain=AS	GCA_017901135.1	2891210	2891210	type	True	100.0	1428	1428	95	conclusive
Thiothrix lacustris	strain=DSM 21227	GCA_000621325.1	525917	525917	type	True	92.7677	968	1428	95	below_threshold
Thiothrix fructosivorans	strain=ATCC 49748	GCA_017349355.1	111770	111770	type	True	82.2251	814	1428	95	below_threshold
Thiothrix subterranea	strain=Ku-5	GCA_016772315.1	2735563	2735563	type	True	82.1848	801	1428	95	below_threshold
Thiothrix winogradskyi	strain=CT3	GCA_021650935.1	96472	96472	type	True	81.6554	816	1428	95	below_threshold
Thiothrix caldifontis	strain=DSM 21228	GCA_900107695.1	525918	525918	type	True	81.5537	736	1428	95	below_threshold
Thiothrix unzii	strain=A1	GCA_017901175.1	111769	111769	type	True	80.993	527	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:11,197] [INFO] DFAST Taxonomy check result was written to GCF_017901135.1_ASM1790113v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:11,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:11,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:11,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe36141e-8912-4edf-b011-2c6ef97b11aa/dqc_reference/checkm_data
[2024-01-24 13:50:11,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:11,238] [INFO] Task started: CheckM
[2024-01-24 13:50:11,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017901135.1_ASM1790113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017901135.1_ASM1790113v1_genomic.fna/checkm_input GCF_017901135.1_ASM1790113v1_genomic.fna/checkm_result
[2024-01-24 13:50:58,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:58,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:58,380] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:58,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:58,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017901135.1_ASM1790113v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:58,381] [INFO] Task started: Blastn
[2024-01-24 13:50:58,381] [INFO] Running command: blastn -query GCF_017901135.1_ASM1790113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe36141e-8912-4edf-b011-2c6ef97b11aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_017901135.1_ASM1790113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:59,538] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:59,543] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:59,543] [INFO] Target genome list was writen to GCF_017901135.1_ASM1790113v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:59,557] [INFO] Task started: fastANI
[2024-01-24 13:50:59,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d17175-26f7-4052-88f4-33b5e9c827c0/GCF_017901135.1_ASM1790113v1_genomic.fna.gz --refList GCF_017901135.1_ASM1790113v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017901135.1_ASM1790113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:09,839] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:09,852] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:09,852] [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_017901135.1	s__Thiothrix sp017901135	100.0	1428	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000621325.1	s__Thiothrix lacustris	92.7679	968	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349355.1	s__Thiothrix fructosivorans	82.2232	814	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772315.1	s__Thiothrix sp016772315	82.1818	797	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107695.1	s__Thiothrix caldifontis	81.5716	734	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017901175.1	s__Thiothrix unzii	80.9785	526	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017901155.1	s__Thiothrix sp017901155	80.3671	469	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822845.1	s__Thiothrix sp018822845	80.1466	580	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	99.95	99.95	0.96	0.95	3	-
GCA_002425225.1	s__Thiothrix moscowensis	79.8111	575	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	99.11	97.35	0.95	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:09,854] [INFO] GTDB search result was written to GCF_017901135.1_ASM1790113v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:09,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:09,857] [INFO] DFAST_QC result json was written to GCF_017901135.1_ASM1790113v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:09,857] [INFO] DFAST_QC completed!
[2024-01-24 13:51:09,857] [INFO] Total running time: 0h1m29s