[2024-01-24 13:36:45,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcb93ea8-e937-4572-b76c-aed00ea18748/dqc_reference
[2024-01-24 13:36:46,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,682] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg284ac450-63f5-429f-a378-dc5db02ea923/GCF_000020005.1_ASM2000v1_genomic.fna.gz | prodigal -d GCF_000020005.1_ASM2000v1_genomic.fna/cds.fna -a GCF_000020005.1_ASM2000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:52,677] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:52,678] [INFO] Task started: HMMsearch
[2024-01-24 13:36:52,678] [INFO] Running command: hmmsearch --tblout GCF_000020005.1_ASM2000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcb93ea8-e937-4572-b76c-aed00ea18748/dqc_reference/reference_markers.hmm GCF_000020005.1_ASM2000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:52,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:52,968] [INFO] Found 6/6 markers.
[2024-01-24 13:36:53,005] [INFO] Query marker FASTA was written to GCF_000020005.1_ASM2000v1_genomic.fna/markers.fasta
[2024-01-24 13:36:53,005] [INFO] Task started: Blastn
[2024-01-24 13:36:53,005] [INFO] Running command: blastn -query GCF_000020005.1_ASM2000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb93ea8-e937-4572-b76c-aed00ea18748/dqc_reference/reference_markers.fasta -out GCF_000020005.1_ASM2000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:53,570] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:53,573] [INFO] Selected 13 target genomes.
[2024-01-24 13:36:53,574] [INFO] Target genome list was writen to GCF_000020005.1_ASM2000v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:53,594] [INFO] Task started: fastANI
[2024-01-24 13:36:53,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg284ac450-63f5-429f-a378-dc5db02ea923/GCF_000020005.1_ASM2000v1_genomic.fna.gz --refList GCF_000020005.1_ASM2000v1_genomic.fna/target_genomes.txt --output GCF_000020005.1_ASM2000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:01,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:01,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcb93ea8-e937-4572-b76c-aed00ea18748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:01,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcb93ea8-e937-4572-b76c-aed00ea18748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:01,468] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:01,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:01,468] [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
Natranaerobius thermophilus	strain=JW/NM-WN-LF	GCA_000020005.1	375929	375929	type	True	100.0	1061	1062	95	conclusive
Natranaerobius trueperi	strain=DSM 18760	GCA_002216005.1	759412	759412	type	True	77.5911	115	1062	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:01,470] [INFO] DFAST Taxonomy check result was written to GCF_000020005.1_ASM2000v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:01,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:01,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:01,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcb93ea8-e937-4572-b76c-aed00ea18748/dqc_reference/checkm_data
[2024-01-24 13:37:01,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:01,504] [INFO] Task started: CheckM
[2024-01-24 13:37:01,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020005.1_ASM2000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020005.1_ASM2000v1_genomic.fna/checkm_input GCF_000020005.1_ASM2000v1_genomic.fna/checkm_result
[2024-01-24 13:37:27,990] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:27,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:28,035] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:28,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:28,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020005.1_ASM2000v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:28,037] [INFO] Task started: Blastn
[2024-01-24 13:37:28,037] [INFO] Running command: blastn -query GCF_000020005.1_ASM2000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb93ea8-e937-4572-b76c-aed00ea18748/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020005.1_ASM2000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:28,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:28,894] [INFO] Selected 16 target genomes.
[2024-01-24 13:37:28,894] [INFO] Target genome list was writen to GCF_000020005.1_ASM2000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:28,939] [INFO] Task started: fastANI
[2024-01-24 13:37:28,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg284ac450-63f5-429f-a378-dc5db02ea923/GCF_000020005.1_ASM2000v1_genomic.fna.gz --refList GCF_000020005.1_ASM2000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020005.1_ASM2000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:38,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:39,006] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:39,006] [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_000020005.1	s__Natranaerobius thermophilus	100.0	1061	1062	d__Bacteria;p__Firmicutes_D;c__Natranaerobiia;o__Natranaerobiales;f__Natranaerobiaceae;g__Natranaerobius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002216005.1	s__Natranaerobius_A trueperi	77.526	117	1062	d__Bacteria;p__Firmicutes_D;c__Natranaerobiia;o__Natranaerobiales;f__Natranaerobiaceae;g__Natranaerobius_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,008] [INFO] GTDB search result was written to GCF_000020005.1_ASM2000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:39,008] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:39,010] [INFO] DFAST_QC result json was written to GCF_000020005.1_ASM2000v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:39,011] [INFO] DFAST_QC completed!
[2024-01-24 13:37:39,011] [INFO] Total running time: 0h0m54s