[2023-06-27 11:40:34,236] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:40:34,242] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:40:34,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e2229ae-5ba0-4761-b55a-390359382519/dqc_reference
[2023-06-27 11:40:35,665] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:40:35,666] [INFO] Task started: Prodigal
[2023-06-27 11:40:35,667] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd855e1f-5af6-4a93-a742-e8a246d3ddbd/GCA_026989175.1_ASM2698917v1_genomic.fna.gz | prodigal -d GCA_026989175.1_ASM2698917v1_genomic.fna/cds.fna -a GCA_026989175.1_ASM2698917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:40:39,710] [INFO] Task succeeded: Prodigal
[2023-06-27 11:40:39,710] [INFO] Task started: HMMsearch
[2023-06-27 11:40:39,710] [INFO] Running command: hmmsearch --tblout GCA_026989175.1_ASM2698917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e2229ae-5ba0-4761-b55a-390359382519/dqc_reference/reference_markers.hmm GCA_026989175.1_ASM2698917v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:40:39,971] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:40:39,973] [INFO] Found 6/6 markers.
[2023-06-27 11:40:39,997] [INFO] Query marker FASTA was written to GCA_026989175.1_ASM2698917v1_genomic.fna/markers.fasta
[2023-06-27 11:40:39,998] [INFO] Task started: Blastn
[2023-06-27 11:40:39,998] [INFO] Running command: blastn -query GCA_026989175.1_ASM2698917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e2229ae-5ba0-4761-b55a-390359382519/dqc_reference/reference_markers.fasta -out GCA_026989175.1_ASM2698917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:40:40,647] [INFO] Task succeeded: Blastn
[2023-06-27 11:40:40,651] [INFO] Selected 32 target genomes.
[2023-06-27 11:40:40,652] [INFO] Target genome list was writen to GCA_026989175.1_ASM2698917v1_genomic.fna/target_genomes.txt
[2023-06-27 11:40:40,659] [INFO] Task started: fastANI
[2023-06-27 11:40:40,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd855e1f-5af6-4a93-a742-e8a246d3ddbd/GCA_026989175.1_ASM2698917v1_genomic.fna.gz --refList GCA_026989175.1_ASM2698917v1_genomic.fna/target_genomes.txt --output GCA_026989175.1_ASM2698917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:40:57,786] [INFO] Task succeeded: fastANI
[2023-06-27 11:40:57,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e2229ae-5ba0-4761-b55a-390359382519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:40:57,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e2229ae-5ba0-4761-b55a-390359382519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:40:57,796] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:40:57,796] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:40:57,796] [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
Thiomicrorhabdus arctica	strain=DSM 13458	GCA_000381085.1	131540	131540	type	True	77.6971	110	552	95	below_threshold
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	77.1356	62	552	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	77.0377	86	552	95	below_threshold
Thiomicrorhabdus aquaedulcis	strain=HaS4	GCA_004001325.1	2211106	2211106	type	True	77.0188	89	552	95	below_threshold
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	76.9474	50	552	95	below_threshold
Thiosulfatimonas sediminis	strain=aks77	GCA_011398355.1	2675054	2675054	type	True	76.81	53	552	95	below_threshold
Thiomicrorhabdus chilensis	strain=DSM 12352	GCA_000483485.1	63656	63656	type	True	76.638	62	552	95	below_threshold
Thiosulfativibrio zosterae	strain=AkT22	GCA_011398155.1	2675053	2675053	type	True	76.0353	57	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:40:57,799] [INFO] DFAST Taxonomy check result was written to GCA_026989175.1_ASM2698917v1_genomic.fna/tc_result.tsv
[2023-06-27 11:40:57,800] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:40:57,800] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:40:57,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e2229ae-5ba0-4761-b55a-390359382519/dqc_reference/checkm_data
[2023-06-27 11:40:57,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:40:57,829] [INFO] Task started: CheckM
[2023-06-27 11:40:57,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026989175.1_ASM2698917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026989175.1_ASM2698917v1_genomic.fna/checkm_input GCA_026989175.1_ASM2698917v1_genomic.fna/checkm_result
[2023-06-27 11:41:17,922] [INFO] Task succeeded: CheckM
[2023-06-27 11:41:17,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:41:17,947] [INFO] ===== Completeness check finished =====
[2023-06-27 11:41:17,948] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:41:17,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026989175.1_ASM2698917v1_genomic.fna/markers.fasta)
[2023-06-27 11:41:17,949] [INFO] Task started: Blastn
[2023-06-27 11:41:17,949] [INFO] Running command: blastn -query GCA_026989175.1_ASM2698917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e2229ae-5ba0-4761-b55a-390359382519/dqc_reference/reference_markers_gtdb.fasta -out GCA_026989175.1_ASM2698917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:41:18,963] [INFO] Task succeeded: Blastn
[2023-06-27 11:41:18,968] [INFO] Selected 23 target genomes.
[2023-06-27 11:41:18,968] [INFO] Target genome list was writen to GCA_026989175.1_ASM2698917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:41:18,984] [INFO] Task started: fastANI
[2023-06-27 11:41:18,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd855e1f-5af6-4a93-a742-e8a246d3ddbd/GCA_026989175.1_ASM2698917v1_genomic.fna.gz --refList GCA_026989175.1_ASM2698917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026989175.1_ASM2698917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:41:29,273] [INFO] Task succeeded: fastANI
[2023-06-27 11:41:29,285] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:41:29,285] [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_015488565.1	s__Thiomicrorhabdus sp015488565	80.7268	283	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487015.1	s__Thiomicrorhabdus sp015487015	79.1644	295	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487495.1	s__Thiomicrorhabdus sp015487495	78.6535	228	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381085.1	s__Thiomicrorhabdus arctica	77.6971	110	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153955.1	s__Thiomicrorhabdus sp013153955	77.4695	91	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478585.1	s__Thiomicrorhabdus sp000478585	77.2167	112	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006222135.1	s__Thiomicrorhabdus sp006222135	77.1691	95	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001325.1	s__Thiomicrorhabdus aquaedulcis	76.9901	90	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004293625.1	s__Thiomicrorhabdus indica	76.9474	50	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012605.1	s__Hydrogenovibrio crunogenus_A	76.8665	58	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011398355.1	s__Thiomicrorhabdus sp011398355	76.81	53	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938655.1	s__Thiomicrorhabdus sp016938655	76.7932	99	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011398155.1	s__Thiosulfativibrio zosterae	76.0353	57	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiosulfativibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:41:29,288] [INFO] GTDB search result was written to GCA_026989175.1_ASM2698917v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:41:29,288] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:41:29,300] [INFO] DFAST_QC result json was written to GCA_026989175.1_ASM2698917v1_genomic.fna/dqc_result.json
[2023-06-27 11:41:29,301] [INFO] DFAST_QC completed!
[2023-06-27 11:41:29,301] [INFO] Total running time: 0h0m55s