[2024-01-24 13:35:26,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:26,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:26,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0aacd10-5415-42b8-8fe2-401c29882f7f/dqc_reference
[2024-01-24 13:35:27,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:27,636] [INFO] Task started: Prodigal
[2024-01-24 13:35:27,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ebe7a81-15d4-48f9-b982-f885f046aa23/GCF_000381085.1_ASM38108v1_genomic.fna.gz | prodigal -d GCF_000381085.1_ASM38108v1_genomic.fna/cds.fna -a GCF_000381085.1_ASM38108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:33,415] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:33,416] [INFO] Task started: HMMsearch
[2024-01-24 13:35:33,416] [INFO] Running command: hmmsearch --tblout GCF_000381085.1_ASM38108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0aacd10-5415-42b8-8fe2-401c29882f7f/dqc_reference/reference_markers.hmm GCF_000381085.1_ASM38108v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:33,667] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:33,668] [INFO] Found 6/6 markers.
[2024-01-24 13:35:33,696] [INFO] Query marker FASTA was written to GCF_000381085.1_ASM38108v1_genomic.fna/markers.fasta
[2024-01-24 13:35:33,696] [INFO] Task started: Blastn
[2024-01-24 13:35:33,696] [INFO] Running command: blastn -query GCF_000381085.1_ASM38108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0aacd10-5415-42b8-8fe2-401c29882f7f/dqc_reference/reference_markers.fasta -out GCF_000381085.1_ASM38108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:34,386] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:34,389] [INFO] Selected 24 target genomes.
[2024-01-24 13:35:34,390] [INFO] Target genome list was writen to GCF_000381085.1_ASM38108v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:34,534] [INFO] Task started: fastANI
[2024-01-24 13:35:34,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebe7a81-15d4-48f9-b982-f885f046aa23/GCF_000381085.1_ASM38108v1_genomic.fna.gz --refList GCF_000381085.1_ASM38108v1_genomic.fna/target_genomes.txt --output GCF_000381085.1_ASM38108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:45,972] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:45,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0aacd10-5415-42b8-8fe2-401c29882f7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:45,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0aacd10-5415-42b8-8fe2-401c29882f7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:45,982] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:35:45,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:35:45,982] [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	100.0	846	848	95	conclusive
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	78.3466	158	848	95	below_threshold
Thiomicrorhabdus chilensis	strain=DSM 12352	GCA_000483485.1	63656	63656	type	True	77.9645	87	848	95	below_threshold
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	77.7788	113	848	95	below_threshold
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	77.7511	79	848	95	below_threshold
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	77.7467	65	848	95	below_threshold
Thiosulfatimonas sediminis	strain=aks77	GCA_011398355.1	2675054	2675054	type	True	77.6155	68	848	95	below_threshold
Thiomicrorhabdus heinhorstiae	strain=HH1	GCA_013391765.2	2748010	2748010	type	True	77.2415	72	848	95	below_threshold
Hydrogenovibrio kuenenii	strain=DSM 12350	GCA_000526715.1	63658	63658	type	True	77.2215	74	848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:45,984] [INFO] DFAST Taxonomy check result was written to GCF_000381085.1_ASM38108v1_genomic.fna/tc_result.tsv
[2024-01-24 13:35:45,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:45,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:45,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0aacd10-5415-42b8-8fe2-401c29882f7f/dqc_reference/checkm_data
[2024-01-24 13:35:45,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:46,019] [INFO] Task started: CheckM
[2024-01-24 13:35:46,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000381085.1_ASM38108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000381085.1_ASM38108v1_genomic.fna/checkm_input GCF_000381085.1_ASM38108v1_genomic.fna/checkm_result
[2024-01-24 13:36:09,673] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:09,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:09,693] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:09,694] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:09,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000381085.1_ASM38108v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:09,695] [INFO] Task started: Blastn
[2024-01-24 13:36:09,695] [INFO] Running command: blastn -query GCF_000381085.1_ASM38108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0aacd10-5415-42b8-8fe2-401c29882f7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000381085.1_ASM38108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:10,774] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:10,778] [INFO] Selected 14 target genomes.
[2024-01-24 13:36:10,779] [INFO] Target genome list was writen to GCF_000381085.1_ASM38108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:10,837] [INFO] Task started: fastANI
[2024-01-24 13:36:10,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebe7a81-15d4-48f9-b982-f885f046aa23/GCF_000381085.1_ASM38108v1_genomic.fna.gz --refList GCF_000381085.1_ASM38108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000381085.1_ASM38108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:17,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:17,223] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:17,223] [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_000381085.1	s__Thiomicrorhabdus arctica	100.0	847	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006222135.1	s__Thiomicrorhabdus sp006222135	84.6706	503	848	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	78.5195	123	848	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	78.0372	172	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702325.1	s__Thiomicrorhabdus sp000702325	78.0168	146	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488565.1	s__Thiomicrorhabdus sp015488565	77.7959	96	848	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	77.626	115	848	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	77.6176	104	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571465.1	s__Thiomicrorhabdus sp017571465	77.4092	75	848	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	77.3062	119	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391765.2	s__Thiomicrorhabdus sp013391765	77.2053	73	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526715.1	s__Hydrogenovibrio kuenenii	76.9609	74	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484555.1	s__Hydrogenovibrio sp015484555	76.9031	56	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	99.62	99.62	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:17,224] [INFO] GTDB search result was written to GCF_000381085.1_ASM38108v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:17,225] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:17,228] [INFO] DFAST_QC result json was written to GCF_000381085.1_ASM38108v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:17,228] [INFO] DFAST_QC completed!
[2024-01-24 13:36:17,228] [INFO] Total running time: 0h0m51s