[2024-01-24 12:47:28,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:28,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:28,024] [INFO] DQC Reference Directory: /var/lib/cwl/stge4007b86-86af-47c9-a66d-4aed1a095893/dqc_reference
[2024-01-24 12:47:29,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:29,304] [INFO] Task started: Prodigal
[2024-01-24 12:47:29,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg038b420c-da79-4a4f-bc66-0c201b9c9682/GCF_000015205.1_ASM1520v1_genomic.fna.gz | prodigal -d GCF_000015205.1_ASM1520v1_genomic.fna/cds.fna -a GCF_000015205.1_ASM1520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:37,287] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:37,288] [INFO] Task started: HMMsearch
[2024-01-24 12:47:37,288] [INFO] Running command: hmmsearch --tblout GCF_000015205.1_ASM1520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4007b86-86af-47c9-a66d-4aed1a095893/dqc_reference/reference_markers.hmm GCF_000015205.1_ASM1520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:37,486] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:37,487] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg038b420c-da79-4a4f-bc66-0c201b9c9682/GCF_000015205.1_ASM1520v1_genomic.fna.gz]
[2024-01-24 12:47:37,508] [INFO] Query marker FASTA was written to GCF_000015205.1_ASM1520v1_genomic.fna/markers.fasta
[2024-01-24 12:47:37,508] [INFO] Task started: Blastn
[2024-01-24 12:47:37,508] [INFO] Running command: blastn -query GCF_000015205.1_ASM1520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4007b86-86af-47c9-a66d-4aed1a095893/dqc_reference/reference_markers.fasta -out GCF_000015205.1_ASM1520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:38,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:38,031] [INFO] Selected 5 target genomes.
[2024-01-24 12:47:38,031] [INFO] Target genome list was writen to GCF_000015205.1_ASM1520v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:38,034] [INFO] Task started: fastANI
[2024-01-24 12:47:38,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg038b420c-da79-4a4f-bc66-0c201b9c9682/GCF_000015205.1_ASM1520v1_genomic.fna.gz --refList GCF_000015205.1_ASM1520v1_genomic.fna/target_genomes.txt --output GCF_000015205.1_ASM1520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:40,434] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:40,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4007b86-86af-47c9-a66d-4aed1a095893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:40,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4007b86-86af-47c9-a66d-4aed1a095893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:40,441] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:40,441] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:40,441] [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
Pyrobaculum islandicum	strain=DSM 4184	GCA_000015205.1	2277	2277	type	True	100.0	608	608	95	conclusive
Pyrobaculum neutrophilum	strain=V24Sta	GCA_000019805.1	70771	70771	type	True	86.5035	274	608	95	below_threshold
Pyrobaculum arsenaticum	strain=DSM 13514	GCA_000016385.1	121277	121277	type	True	77.7802	58	608	95	below_threshold
Pyrobaculum ferrireducens	strain=1860	GCA_000234805.1	1104324	1104324	type	True	77.711	86	608	95	below_threshold
Pyrobaculum calidifontis	strain=JCM 11548	GCA_000015805.1	181486	181486	type	True	77.0727	63	608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:40,444] [INFO] DFAST Taxonomy check result was written to GCF_000015205.1_ASM1520v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:40,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:40,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:40,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4007b86-86af-47c9-a66d-4aed1a095893/dqc_reference/checkm_data
[2024-01-24 12:47:40,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:40,470] [INFO] Task started: CheckM
[2024-01-24 12:47:40,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015205.1_ASM1520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015205.1_ASM1520v1_genomic.fna/checkm_input GCF_000015205.1_ASM1520v1_genomic.fna/checkm_result
[2024-01-24 12:48:08,374] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:08,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:08,395] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:08,395] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:08,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015205.1_ASM1520v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:08,396] [INFO] Task started: Blastn
[2024-01-24 12:48:08,396] [INFO] Running command: blastn -query GCF_000015205.1_ASM1520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4007b86-86af-47c9-a66d-4aed1a095893/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015205.1_ASM1520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:08,881] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:08,884] [INFO] Selected 5 target genomes.
[2024-01-24 12:48:08,885] [INFO] Target genome list was writen to GCF_000015205.1_ASM1520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:08,904] [INFO] Task started: fastANI
[2024-01-24 12:48:08,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg038b420c-da79-4a4f-bc66-0c201b9c9682/GCF_000015205.1_ASM1520v1_genomic.fna.gz --refList GCF_000015205.1_ASM1520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015205.1_ASM1520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:11,505] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:11,510] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:11,511] [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_000015205.1	s__Pyrobaculum islandicum	100.0	608	608	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000019805.1	s__Pyrobaculum neutrophilum	86.5464	273	608	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000234805.1	s__Pyrobaculum ferrireducens	77.7193	87	608	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000247545.1	s__Pyrobaculum oguniense	77.1597	61	608	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum	95.9585	N/A	N/A	N/A	N/A	1	-
GCF_000015805.1	s__Pyrobaculum calidifontis	77.0329	61	608	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:11,513] [INFO] GTDB search result was written to GCF_000015205.1_ASM1520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:11,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:11,516] [INFO] DFAST_QC result json was written to GCF_000015205.1_ASM1520v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:11,516] [INFO] DFAST_QC completed!
[2024-01-24 12:48:11,516] [INFO] Total running time: 0h0m43s