[2024-01-25 18:33:20,842] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:20,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:20,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg44241249-5413-4632-b892-324a6c610508/dqc_reference
[2024-01-25 18:33:22,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:22,040] [INFO] Task started: Prodigal
[2024-01-25 18:33:22,040] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbabe29c-2f98-44fe-a1aa-edc8af06d709/GCF_011398355.1_ASM1139835v1_genomic.fna.gz | prodigal -d GCF_011398355.1_ASM1139835v1_genomic.fna/cds.fna -a GCF_011398355.1_ASM1139835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:28,328] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:28,328] [INFO] Task started: HMMsearch
[2024-01-25 18:33:28,328] [INFO] Running command: hmmsearch --tblout GCF_011398355.1_ASM1139835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44241249-5413-4632-b892-324a6c610508/dqc_reference/reference_markers.hmm GCF_011398355.1_ASM1139835v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:28,536] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:28,537] [INFO] Found 6/6 markers.
[2024-01-25 18:33:28,561] [INFO] Query marker FASTA was written to GCF_011398355.1_ASM1139835v1_genomic.fna/markers.fasta
[2024-01-25 18:33:28,561] [INFO] Task started: Blastn
[2024-01-25 18:33:28,561] [INFO] Running command: blastn -query GCF_011398355.1_ASM1139835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44241249-5413-4632-b892-324a6c610508/dqc_reference/reference_markers.fasta -out GCF_011398355.1_ASM1139835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:29,172] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:29,175] [INFO] Selected 26 target genomes.
[2024-01-25 18:33:29,175] [INFO] Target genome list was writen to GCF_011398355.1_ASM1139835v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:29,268] [INFO] Task started: fastANI
[2024-01-25 18:33:29,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbabe29c-2f98-44fe-a1aa-edc8af06d709/GCF_011398355.1_ASM1139835v1_genomic.fna.gz --refList GCF_011398355.1_ASM1139835v1_genomic.fna/target_genomes.txt --output GCF_011398355.1_ASM1139835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:33:44,511] [INFO] Task succeeded: fastANI
[2024-01-25 18:33:44,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44241249-5413-4632-b892-324a6c610508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:33:44,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44241249-5413-4632-b892-324a6c610508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:33:44,518] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:33:44,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:33:44,518] [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
Thiosulfatimonas sediminis	strain=aks77	GCA_011398355.1	2675054	2675054	type	True	100.0	904	907	95	conclusive
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	79.1283	153	907	95	below_threshold
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	79.0372	209	907	95	below_threshold
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	78.8142	127	907	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	78.3985	122	907	95	below_threshold
Thiomicrospira aerophila	strain=AL3	GCA_000227665.3	92245	92245	type	True	77.838	58	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:33:44,520] [INFO] DFAST Taxonomy check result was written to GCF_011398355.1_ASM1139835v1_genomic.fna/tc_result.tsv
[2024-01-25 18:33:44,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:33:44,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:33:44,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44241249-5413-4632-b892-324a6c610508/dqc_reference/checkm_data
[2024-01-25 18:33:44,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:33:44,552] [INFO] Task started: CheckM
[2024-01-25 18:33:44,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011398355.1_ASM1139835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011398355.1_ASM1139835v1_genomic.fna/checkm_input GCF_011398355.1_ASM1139835v1_genomic.fna/checkm_result
[2024-01-25 18:34:08,147] [INFO] Task succeeded: CheckM
[2024-01-25 18:34:08,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:34:08,165] [INFO] ===== Completeness check finished =====
[2024-01-25 18:34:08,166] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:34:08,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011398355.1_ASM1139835v1_genomic.fna/markers.fasta)
[2024-01-25 18:34:08,167] [INFO] Task started: Blastn
[2024-01-25 18:34:08,167] [INFO] Running command: blastn -query GCF_011398355.1_ASM1139835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44241249-5413-4632-b892-324a6c610508/dqc_reference/reference_markers_gtdb.fasta -out GCF_011398355.1_ASM1139835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:34:09,212] [INFO] Task succeeded: Blastn
[2024-01-25 18:34:09,214] [INFO] Selected 21 target genomes.
[2024-01-25 18:34:09,214] [INFO] Target genome list was writen to GCF_011398355.1_ASM1139835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:34:09,242] [INFO] Task started: fastANI
[2024-01-25 18:34:09,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbabe29c-2f98-44fe-a1aa-edc8af06d709/GCF_011398355.1_ASM1139835v1_genomic.fna.gz --refList GCF_011398355.1_ASM1139835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011398355.1_ASM1139835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:34:21,630] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:21,639] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:34:21,639] [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_011398355.1	s__Thiomicrorhabdus sp011398355	100.0	905	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017571465.1	s__Thiomicrorhabdus sp017571465	79.2337	366	907	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	79.1141	154	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282625.1	s__Thiomicrorhabdus xiamenensis	78.9643	208	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885815.1	s__Thiomicrorhabdus sediminis	78.7681	126	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571475.1	s__Thiomicrorhabdus sp017571475	78.4669	199	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936535.1	s__Thiomicrorhabdus sp016936535	78.3826	163	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227665.2	s__Thiomicrospira aerophila	77.957	59	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001325.1	s__Thiomicrorhabdus aquaedulcis	77.8552	102	907	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	76.7603	111	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299245.1	s__Thiomicrorhabdus sp002299245	76.7157	54	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.68	99.68	0.83	0.83	2	-
GCA_015487495.1	s__Thiomicrorhabdus sp015487495	76.3794	57	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:34:21,641] [INFO] GTDB search result was written to GCF_011398355.1_ASM1139835v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:34:21,641] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:34:21,644] [INFO] DFAST_QC result json was written to GCF_011398355.1_ASM1139835v1_genomic.fna/dqc_result.json
[2024-01-25 18:34:21,645] [INFO] DFAST_QC completed!
[2024-01-25 18:34:21,645] [INFO] Total running time: 0h1m1s