[2024-01-25 19:49:20,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,529] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8edc60d-4d81-43c3-9d32-63e9775c08fc/dqc_reference
[2024-01-25 19:49:21,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:21,722] [INFO] Task started: Prodigal
[2024-01-25 19:49:21,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg979c4740-fd45-4d82-8226-978320584c0b/GCF_021650935.1_ASM2165093v1_genomic.fna.gz | prodigal -d GCF_021650935.1_ASM2165093v1_genomic.fna/cds.fna -a GCF_021650935.1_ASM2165093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:34,366] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:34,366] [INFO] Task started: HMMsearch
[2024-01-25 19:49:34,366] [INFO] Running command: hmmsearch --tblout GCF_021650935.1_ASM2165093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8edc60d-4d81-43c3-9d32-63e9775c08fc/dqc_reference/reference_markers.hmm GCF_021650935.1_ASM2165093v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:34,687] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:34,688] [INFO] Found 6/6 markers.
[2024-01-25 19:49:34,732] [INFO] Query marker FASTA was written to GCF_021650935.1_ASM2165093v1_genomic.fna/markers.fasta
[2024-01-25 19:49:34,732] [INFO] Task started: Blastn
[2024-01-25 19:49:34,732] [INFO] Running command: blastn -query GCF_021650935.1_ASM2165093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8edc60d-4d81-43c3-9d32-63e9775c08fc/dqc_reference/reference_markers.fasta -out GCF_021650935.1_ASM2165093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:35,340] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:35,343] [INFO] Selected 12 target genomes.
[2024-01-25 19:49:35,344] [INFO] Target genome list was writen to GCF_021650935.1_ASM2165093v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:35,359] [INFO] Task started: fastANI
[2024-01-25 19:49:35,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg979c4740-fd45-4d82-8226-978320584c0b/GCF_021650935.1_ASM2165093v1_genomic.fna.gz --refList GCF_021650935.1_ASM2165093v1_genomic.fna/target_genomes.txt --output GCF_021650935.1_ASM2165093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:46,959] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:46,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8edc60d-4d81-43c3-9d32-63e9775c08fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:46,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8edc60d-4d81-43c3-9d32-63e9775c08fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:46,966] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:46,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:46,966] [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 winogradskyi	strain=CT3	GCA_021650935.1	96472	96472	type	True	100.0	1457	1458	95	conclusive
Thiothrix subterranea	strain=Ku-5	GCA_016772315.1	2735563	2735563	type	True	89.2462	994	1458	95	below_threshold
Thiothrix caldifontis	strain=DSM 21228	GCA_900107695.1	525918	525918	type	True	85.9317	874	1458	95	below_threshold
Thiothrix fructosivorans	strain=ATCC 49748	GCA_017349355.1	111770	111770	type	True	83.7664	881	1458	95	below_threshold
Thiothrix unzii	strain=A1	GCA_017901175.1	111769	111769	type	True	83.464	593	1458	95	below_threshold
Thiothrix litoralis	strain=AS	GCA_017901135.1	2891210	2891210	type	True	81.6629	808	1458	95	below_threshold
Thiothrix lacustris	strain=DSM 21227	GCA_000621325.1	525917	525917	type	True	81.5507	723	1458	95	below_threshold
Thiothrix nivea	strain=DSM 5205	GCA_000260135.1	1031	1031	type	True	78.7461	517	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:46,968] [INFO] DFAST Taxonomy check result was written to GCF_021650935.1_ASM2165093v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:46,968] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:46,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:46,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8edc60d-4d81-43c3-9d32-63e9775c08fc/dqc_reference/checkm_data
[2024-01-25 19:49:46,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:47,009] [INFO] Task started: CheckM
[2024-01-25 19:49:47,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021650935.1_ASM2165093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021650935.1_ASM2165093v1_genomic.fna/checkm_input GCF_021650935.1_ASM2165093v1_genomic.fna/checkm_result
[2024-01-25 19:50:27,002] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:27,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:27,024] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:27,024] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:27,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021650935.1_ASM2165093v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:27,025] [INFO] Task started: Blastn
[2024-01-25 19:50:27,025] [INFO] Running command: blastn -query GCF_021650935.1_ASM2165093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8edc60d-4d81-43c3-9d32-63e9775c08fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_021650935.1_ASM2165093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:27,877] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:27,879] [INFO] Selected 9 target genomes.
[2024-01-25 19:50:27,879] [INFO] Target genome list was writen to GCF_021650935.1_ASM2165093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:27,891] [INFO] Task started: fastANI
[2024-01-25 19:50:27,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg979c4740-fd45-4d82-8226-978320584c0b/GCF_021650935.1_ASM2165093v1_genomic.fna.gz --refList GCF_021650935.1_ASM2165093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021650935.1_ASM2165093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:36,537] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:36,544] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:50:36,544] [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_016772315.1	s__Thiothrix sp016772315	89.255	994	1458	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	85.9429	872	1458	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	85.1261	578	1458	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	83.7836	880	1458	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	83.4826	592	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017901135.1	s__Thiothrix sp017901135	81.6399	814	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621325.1	s__Thiothrix lacustris	81.5476	723	1458	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	79.8939	485	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	99.95	99.95	0.96	0.95	3	-
GCF_000260135.1	s__Thiothrix nivea	78.7414	518	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:36,545] [INFO] GTDB search result was written to GCF_021650935.1_ASM2165093v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:36,546] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:36,548] [INFO] DFAST_QC result json was written to GCF_021650935.1_ASM2165093v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:36,549] [INFO] DFAST_QC completed!
[2024-01-25 19:50:36,549] [INFO] Total running time: 0h1m16s