[2024-01-24 12:14:49,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,228] [INFO] DQC Reference Directory: /var/lib/cwl/stgf92e4a6a-3ad8-4dc4-a44c-861d2b0291f0/dqc_reference
[2024-01-24 12:14:50,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,601] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ba96342-ac03-45f4-a10d-e931c9f4c706/GCF_017873965.1_ASM1787396v1_genomic.fna.gz | prodigal -d GCF_017873965.1_ASM1787396v1_genomic.fna/cds.fna -a GCF_017873965.1_ASM1787396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:03,060] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:03,061] [INFO] Task started: HMMsearch
[2024-01-24 12:15:03,061] [INFO] Running command: hmmsearch --tblout GCF_017873965.1_ASM1787396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf92e4a6a-3ad8-4dc4-a44c-861d2b0291f0/dqc_reference/reference_markers.hmm GCF_017873965.1_ASM1787396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:03,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:03,404] [INFO] Found 6/6 markers.
[2024-01-24 12:15:03,461] [INFO] Query marker FASTA was written to GCF_017873965.1_ASM1787396v1_genomic.fna/markers.fasta
[2024-01-24 12:15:03,462] [INFO] Task started: Blastn
[2024-01-24 12:15:03,462] [INFO] Running command: blastn -query GCF_017873965.1_ASM1787396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf92e4a6a-3ad8-4dc4-a44c-861d2b0291f0/dqc_reference/reference_markers.fasta -out GCF_017873965.1_ASM1787396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,088] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,092] [INFO] Selected 25 target genomes.
[2024-01-24 12:15:04,092] [INFO] Target genome list was writen to GCF_017873965.1_ASM1787396v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:04,101] [INFO] Task started: fastANI
[2024-01-24 12:15:04,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba96342-ac03-45f4-a10d-e931c9f4c706/GCF_017873965.1_ASM1787396v1_genomic.fna.gz --refList GCF_017873965.1_ASM1787396v1_genomic.fna/target_genomes.txt --output GCF_017873965.1_ASM1787396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:19,993] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:19,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf92e4a6a-3ad8-4dc4-a44c-861d2b0291f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:19,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf92e4a6a-3ad8-4dc4-a44c-861d2b0291f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:19,997] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:19,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:19,997] [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
Ammoniphilus resinae	strain=DSM 24738	GCA_017873965.1	861532	861532	type	True	100.0	1629	1631	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,999] [INFO] DFAST Taxonomy check result was written to GCF_017873965.1_ASM1787396v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:20,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:20,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:20,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf92e4a6a-3ad8-4dc4-a44c-861d2b0291f0/dqc_reference/checkm_data
[2024-01-24 12:15:20,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:20,055] [INFO] Task started: CheckM
[2024-01-24 12:15:20,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873965.1_ASM1787396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873965.1_ASM1787396v1_genomic.fna/checkm_input GCF_017873965.1_ASM1787396v1_genomic.fna/checkm_result
[2024-01-24 12:15:59,015] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:59,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:59,046] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:59,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:59,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873965.1_ASM1787396v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:59,047] [INFO] Task started: Blastn
[2024-01-24 12:15:59,047] [INFO] Running command: blastn -query GCF_017873965.1_ASM1787396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf92e4a6a-3ad8-4dc4-a44c-861d2b0291f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873965.1_ASM1787396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:59,811] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:59,815] [INFO] Selected 29 target genomes.
[2024-01-24 12:15:59,815] [INFO] Target genome list was writen to GCF_017873965.1_ASM1787396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:59,845] [INFO] Task started: fastANI
[2024-01-24 12:15:59,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba96342-ac03-45f4-a10d-e931c9f4c706/GCF_017873965.1_ASM1787396v1_genomic.fna.gz --refList GCF_017873965.1_ASM1787396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873965.1_ASM1787396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:16,881] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:16,886] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:16,886] [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_017873965.1	s__Ammoniphilus_A resinae	100.0	1629	1631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__RAOX-1;g__Ammoniphilus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:16:16,888] [INFO] GTDB search result was written to GCF_017873965.1_ASM1787396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:16,889] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:16,892] [INFO] DFAST_QC result json was written to GCF_017873965.1_ASM1787396v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:16,892] [INFO] DFAST_QC completed!
[2024-01-24 12:16:16,892] [INFO] Total running time: 0h1m28s