[2024-01-24 12:31:51,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,348] [INFO] DQC Reference Directory: /var/lib/cwl/stga13dc3b9-e7c7-4c10-955e-9a1780dcb3b9/dqc_reference
[2024-01-24 12:31:52,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,616] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,616] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf337597-83a8-4623-bd87-cbea17c5d961/GCF_000024605.1_ASM2460v1_genomic.fna.gz | prodigal -d GCF_000024605.1_ASM2460v1_genomic.fna/cds.fna -a GCF_000024605.1_ASM2460v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:58,276] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:58,277] [INFO] Task started: HMMsearch
[2024-01-24 12:31:58,277] [INFO] Running command: hmmsearch --tblout GCF_000024605.1_ASM2460v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga13dc3b9-e7c7-4c10-955e-9a1780dcb3b9/dqc_reference/reference_markers.hmm GCF_000024605.1_ASM2460v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:58,515] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:58,517] [INFO] Found 6/6 markers.
[2024-01-24 12:31:58,547] [INFO] Query marker FASTA was written to GCF_000024605.1_ASM2460v1_genomic.fna/markers.fasta
[2024-01-24 12:31:58,548] [INFO] Task started: Blastn
[2024-01-24 12:31:58,548] [INFO] Running command: blastn -query GCF_000024605.1_ASM2460v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga13dc3b9-e7c7-4c10-955e-9a1780dcb3b9/dqc_reference/reference_markers.fasta -out GCF_000024605.1_ASM2460v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:59,137] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:59,140] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:59,141] [INFO] Target genome list was writen to GCF_000024605.1_ASM2460v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:59,151] [INFO] Task started: fastANI
[2024-01-24 12:31:59,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf337597-83a8-4623-bd87-cbea17c5d961/GCF_000024605.1_ASM2460v1_genomic.fna.gz --refList GCF_000024605.1_ASM2460v1_genomic.fna/target_genomes.txt --output GCF_000024605.1_ASM2460v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:07,614] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:07,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga13dc3b9-e7c7-4c10-955e-9a1780dcb3b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:07,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga13dc3b9-e7c7-4c10-955e-9a1780dcb3b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:07,621] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:07,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:07,621] [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
Ammonifex degensii	strain=KC4	GCA_000024605.1	42838	42838	type	True	100.0	718	718	95	conclusive
Ammonifex thiophilus	strain=SR	GCA_003368535.1	444093	444093	type	True	88.7093	524	718	95	below_threshold
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	78.0058	91	718	95	below_threshold
Thermodesulfitimonas autotrophica	strain=DSM 102936	GCA_003815015.1	1894989	1894989	type	True	77.8715	59	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:07,623] [INFO] DFAST Taxonomy check result was written to GCF_000024605.1_ASM2460v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:07,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:07,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:07,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga13dc3b9-e7c7-4c10-955e-9a1780dcb3b9/dqc_reference/checkm_data
[2024-01-24 12:32:07,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:07,654] [INFO] Task started: CheckM
[2024-01-24 12:32:07,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024605.1_ASM2460v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024605.1_ASM2460v1_genomic.fna/checkm_input GCF_000024605.1_ASM2460v1_genomic.fna/checkm_result
[2024-01-24 12:32:29,950] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:29,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:29,973] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:29,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:29,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024605.1_ASM2460v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:29,974] [INFO] Task started: Blastn
[2024-01-24 12:32:29,974] [INFO] Running command: blastn -query GCF_000024605.1_ASM2460v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga13dc3b9-e7c7-4c10-955e-9a1780dcb3b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024605.1_ASM2460v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:30,863] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:30,868] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:30,869] [INFO] Target genome list was writen to GCF_000024605.1_ASM2460v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:30,916] [INFO] Task started: fastANI
[2024-01-24 12:32:30,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf337597-83a8-4623-bd87-cbea17c5d961/GCF_000024605.1_ASM2460v1_genomic.fna.gz --refList GCF_000024605.1_ASM2460v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024605.1_ASM2460v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:39,740] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:39,745] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:39,745] [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_000024605.1	s__Ammonifex degensii	100.0	718	718	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Ammonifex	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003368535.1	s__Ammonifex thiophilus	88.678	525	718	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Ammonifex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815015.1	s__Thermodesulfitimonas autotrophica	77.8715	59	718	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Thermodesulfitimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:39,748] [INFO] GTDB search result was written to GCF_000024605.1_ASM2460v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:39,749] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:39,752] [INFO] DFAST_QC result json was written to GCF_000024605.1_ASM2460v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:39,753] [INFO] DFAST_QC completed!
[2024-01-24 12:32:39,753] [INFO] Total running time: 0h0m48s