[2024-01-24 14:28:17,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg37203c39-a92d-4cbb-b737-7c5956b54c75/dqc_reference
[2024-01-24 14:28:20,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,481] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,481] [INFO] Running command: gunzip -c /var/lib/cwl/stgf26043ec-77e4-4e03-8521-633653a9ed4d/GCF_000227665.2_ASM22766v3_genomic.fna.gz | prodigal -d GCF_000227665.2_ASM22766v3_genomic.fna/cds.fna -a GCF_000227665.2_ASM22766v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:26,283] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:26,284] [INFO] Task started: HMMsearch
[2024-01-24 14:28:26,284] [INFO] Running command: hmmsearch --tblout GCF_000227665.2_ASM22766v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37203c39-a92d-4cbb-b737-7c5956b54c75/dqc_reference/reference_markers.hmm GCF_000227665.2_ASM22766v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:26,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:26,545] [INFO] Found 6/6 markers.
[2024-01-24 14:28:26,570] [INFO] Query marker FASTA was written to GCF_000227665.2_ASM22766v3_genomic.fna/markers.fasta
[2024-01-24 14:28:26,571] [INFO] Task started: Blastn
[2024-01-24 14:28:26,571] [INFO] Running command: blastn -query GCF_000227665.2_ASM22766v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg37203c39-a92d-4cbb-b737-7c5956b54c75/dqc_reference/reference_markers.fasta -out GCF_000227665.2_ASM22766v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:27,291] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:27,294] [INFO] Selected 24 target genomes.
[2024-01-24 14:28:27,294] [INFO] Target genome list was writen to GCF_000227665.2_ASM22766v3_genomic.fna/target_genomes.txt
[2024-01-24 14:28:27,307] [INFO] Task started: fastANI
[2024-01-24 14:28:27,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgf26043ec-77e4-4e03-8521-633653a9ed4d/GCF_000227665.2_ASM22766v3_genomic.fna.gz --refList GCF_000227665.2_ASM22766v3_genomic.fna/target_genomes.txt --output GCF_000227665.2_ASM22766v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:40,761] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:40,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37203c39-a92d-4cbb-b737-7c5956b54c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:40,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37203c39-a92d-4cbb-b737-7c5956b54c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:40,769] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:40,770] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:40,770] [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
Thiomicrospira aerophila	strain=AL3	GCA_000227665.3	92245	92245	type	True	100.0	718	719	95	conclusive
Thiomicrospira cyclica	strain=ALM1	GCA_000214825.1	147268	147268	type	True	80.6957	366	719	95	below_threshold
Hydrogenovibrio marinus	strain=MH-110	GCA_013340845.1	28885	28885	type	True	78.0604	51	719	95	below_threshold
Hydrogenovibrio marinus	strain=DSM 11271	GCA_000711315.1	28885	28885	type	True	78.0415	50	719	95	below_threshold
Thiomicrospira pelophila	strain=DSM 1534	GCA_000711195.1	934	934	type	True	77.9764	130	719	95	below_threshold
Thiosulfatimonas sediminis	strain=aks77	GCA_011398355.1	2675054	2675054	type	True	77.7681	54	719	95	below_threshold
Thiomicrospira microaerophila	strain=ASL8-2	GCA_000934765.1	406020	406020	type	True	77.7055	150	719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:40,772] [INFO] DFAST Taxonomy check result was written to GCF_000227665.2_ASM22766v3_genomic.fna/tc_result.tsv
[2024-01-24 14:28:40,772] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:40,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:40,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37203c39-a92d-4cbb-b737-7c5956b54c75/dqc_reference/checkm_data
[2024-01-24 14:28:40,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:40,801] [INFO] Task started: CheckM
[2024-01-24 14:28:40,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000227665.2_ASM22766v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000227665.2_ASM22766v3_genomic.fna/checkm_input GCF_000227665.2_ASM22766v3_genomic.fna/checkm_result
[2024-01-24 14:29:04,184] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:04,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:04,203] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:04,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:04,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000227665.2_ASM22766v3_genomic.fna/markers.fasta)
[2024-01-24 14:29:04,204] [INFO] Task started: Blastn
[2024-01-24 14:29:04,204] [INFO] Running command: blastn -query GCF_000227665.2_ASM22766v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg37203c39-a92d-4cbb-b737-7c5956b54c75/dqc_reference/reference_markers_gtdb.fasta -out GCF_000227665.2_ASM22766v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:05,369] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:05,374] [INFO] Selected 19 target genomes.
[2024-01-24 14:29:05,374] [INFO] Target genome list was writen to GCF_000227665.2_ASM22766v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:05,391] [INFO] Task started: fastANI
[2024-01-24 14:29:05,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgf26043ec-77e4-4e03-8521-633653a9ed4d/GCF_000227665.2_ASM22766v3_genomic.fna.gz --refList GCF_000227665.2_ASM22766v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000227665.2_ASM22766v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:16,955] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:16,969] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:16,969] [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_000227665.2	s__Thiomicrospira aerophila	100.0	719	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112445.1	s__Thiomicrospira sp900112445	87.648	527	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214825.1	s__Thiomicrospira cyclica	80.6957	366	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711195.1	s__Thiomicrospira pelophila	78.006	130	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934765.1	s__Thiomicrospira microaerophila	77.7239	149	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859555.1	s__Thiomicrospira sp014859555	77.6555	134	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011398355.1	s__Thiomicrorhabdus sp011398355	77.4959	53	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421475.1	s__Thiomicrospira sp002421475	77.2001	120	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:16,971] [INFO] GTDB search result was written to GCF_000227665.2_ASM22766v3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:16,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:16,974] [INFO] DFAST_QC result json was written to GCF_000227665.2_ASM22766v3_genomic.fna/dqc_result.json
[2024-01-24 14:29:16,975] [INFO] DFAST_QC completed!
[2024-01-24 14:29:16,975] [INFO] Total running time: 0h0m59s