[2024-01-25 18:53:05,808] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,809] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg42cf5208-b9d2-4261-8e85-41b896e6870d/dqc_reference
[2024-01-25 18:53:07,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:07,008] [INFO] Task started: Prodigal
[2024-01-25 18:53:07,008] [INFO] Running command: gunzip -c /var/lib/cwl/stgae91bc08-a14e-4888-9fac-52e241759deb/GCF_000373545.1_ASM37354v1_genomic.fna.gz | prodigal -d GCF_000373545.1_ASM37354v1_genomic.fna/cds.fna -a GCF_000373545.1_ASM37354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:14,530] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:14,530] [INFO] Task started: HMMsearch
[2024-01-25 18:53:14,530] [INFO] Running command: hmmsearch --tblout GCF_000373545.1_ASM37354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42cf5208-b9d2-4261-8e85-41b896e6870d/dqc_reference/reference_markers.hmm GCF_000373545.1_ASM37354v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:14,730] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:14,731] [INFO] Found 6/6 markers.
[2024-01-25 18:53:14,758] [INFO] Query marker FASTA was written to GCF_000373545.1_ASM37354v1_genomic.fna/markers.fasta
[2024-01-25 18:53:14,758] [INFO] Task started: Blastn
[2024-01-25 18:53:14,759] [INFO] Running command: blastn -query GCF_000373545.1_ASM37354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42cf5208-b9d2-4261-8e85-41b896e6870d/dqc_reference/reference_markers.fasta -out GCF_000373545.1_ASM37354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:15,306] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:15,309] [INFO] Selected 15 target genomes.
[2024-01-25 18:53:15,310] [INFO] Target genome list was writen to GCF_000373545.1_ASM37354v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:15,319] [INFO] Task started: fastANI
[2024-01-25 18:53:15,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgae91bc08-a14e-4888-9fac-52e241759deb/GCF_000373545.1_ASM37354v1_genomic.fna.gz --refList GCF_000373545.1_ASM37354v1_genomic.fna/target_genomes.txt --output GCF_000373545.1_ASM37354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:26,724] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:26,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42cf5208-b9d2-4261-8e85-41b896e6870d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:26,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42cf5208-b9d2-4261-8e85-41b896e6870d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:26,728] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:53:26,728] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:53:26,728] [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
Alkalispirochaeta americana	strain=ASpG1	GCA_900156105.1	159291	159291	type	True	82.9387	811	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:26,730] [INFO] DFAST Taxonomy check result was written to GCF_000373545.1_ASM37354v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:26,730] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:26,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:26,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42cf5208-b9d2-4261-8e85-41b896e6870d/dqc_reference/checkm_data
[2024-01-25 18:53:26,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:26,768] [INFO] Task started: CheckM
[2024-01-25 18:53:26,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000373545.1_ASM37354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000373545.1_ASM37354v1_genomic.fna/checkm_input GCF_000373545.1_ASM37354v1_genomic.fna/checkm_result
[2024-01-25 18:53:53,146] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:53,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:53,182] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:53,183] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:53,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000373545.1_ASM37354v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:53,183] [INFO] Task started: Blastn
[2024-01-25 18:53:53,183] [INFO] Running command: blastn -query GCF_000373545.1_ASM37354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42cf5208-b9d2-4261-8e85-41b896e6870d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000373545.1_ASM37354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:53,970] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:53,974] [INFO] Selected 19 target genomes.
[2024-01-25 18:53:53,974] [INFO] Target genome list was writen to GCF_000373545.1_ASM37354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:54,018] [INFO] Task started: fastANI
[2024-01-25 18:53:54,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgae91bc08-a14e-4888-9fac-52e241759deb/GCF_000373545.1_ASM37354v1_genomic.fna.gz --refList GCF_000373545.1_ASM37354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000373545.1_ASM37354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:06,180] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:06,186] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:06,186] [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_000373545.1	s__Alkalispirochaeta alkalica	100.0	1086	1090	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	98.41	98.41	0.91	0.91	2	conclusive
GCF_900156105.1	s__Alkalispirochaeta americana	82.9391	810	1090	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130865.1	s__Alkalispirochaeta sp007130865	77.1145	130	1090	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	99.39	99.33	0.88	0.87	3	-
GCA_007695175.1	s__Alkalispirochaeta sp007695175	76.9477	143	1090	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117185.1	s__Alkalispirochaeta sp007117185	76.6127	123	1090	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:06,187] [INFO] GTDB search result was written to GCF_000373545.1_ASM37354v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:06,188] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:06,191] [INFO] DFAST_QC result json was written to GCF_000373545.1_ASM37354v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:06,191] [INFO] DFAST_QC completed!
[2024-01-25 18:54:06,191] [INFO] Total running time: 0h1m0s