[2024-01-24 14:03:03,187] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:03,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:03,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg95776166-4e77-44bc-86f9-b38b96454769/dqc_reference
[2024-01-24 14:03:04,469] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:04,470] [INFO] Task started: Prodigal
[2024-01-24 14:03:04,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ae7f641-e3e5-4b9f-89d3-ac34f73643a4/GCF_000378205.1_ASM37820v1_genomic.fna.gz | prodigal -d GCF_000378205.1_ASM37820v1_genomic.fna/cds.fna -a GCF_000378205.1_ASM37820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:16,308] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:16,309] [INFO] Task started: HMMsearch
[2024-01-24 14:03:16,309] [INFO] Running command: hmmsearch --tblout GCF_000378205.1_ASM37820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95776166-4e77-44bc-86f9-b38b96454769/dqc_reference/reference_markers.hmm GCF_000378205.1_ASM37820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:16,691] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:16,692] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3ae7f641-e3e5-4b9f-89d3-ac34f73643a4/GCF_000378205.1_ASM37820v1_genomic.fna.gz]
[2024-01-24 14:03:16,740] [INFO] Query marker FASTA was written to GCF_000378205.1_ASM37820v1_genomic.fna/markers.fasta
[2024-01-24 14:03:16,741] [INFO] Task started: Blastn
[2024-01-24 14:03:16,741] [INFO] Running command: blastn -query GCF_000378205.1_ASM37820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95776166-4e77-44bc-86f9-b38b96454769/dqc_reference/reference_markers.fasta -out GCF_000378205.1_ASM37820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:17,387] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:17,394] [INFO] Selected 9 target genomes.
[2024-01-24 14:03:17,395] [INFO] Target genome list was writen to GCF_000378205.1_ASM37820v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:17,412] [INFO] Task started: fastANI
[2024-01-24 14:03:17,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ae7f641-e3e5-4b9f-89d3-ac34f73643a4/GCF_000378205.1_ASM37820v1_genomic.fna.gz --refList GCF_000378205.1_ASM37820v1_genomic.fna/target_genomes.txt --output GCF_000378205.1_ASM37820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:24,587] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:24,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95776166-4e77-44bc-86f9-b38b96454769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:24,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95776166-4e77-44bc-86f9-b38b96454769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:24,595] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:24,595] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:24,596] [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
Sediminispirochaeta bajacaliforniensis	strain=DSM 16054	GCA_000378205.1	148	148	type	True	100.0	1478	1489	95	conclusive
Sediminispirochaeta smaragdinae	strain=DSM 11293	GCA_000143985.1	55206	55206	type	True	94.5959	1284	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:24,598] [INFO] DFAST Taxonomy check result was written to GCF_000378205.1_ASM37820v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:24,599] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:24,599] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:24,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95776166-4e77-44bc-86f9-b38b96454769/dqc_reference/checkm_data
[2024-01-24 14:03:24,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:24,681] [INFO] Task started: CheckM
[2024-01-24 14:03:24,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378205.1_ASM37820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378205.1_ASM37820v1_genomic.fna/checkm_input GCF_000378205.1_ASM37820v1_genomic.fna/checkm_result
[2024-01-24 14:04:04,087] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:04,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:04,117] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:04,117] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:04,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378205.1_ASM37820v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:04,118] [INFO] Task started: Blastn
[2024-01-24 14:04:04,118] [INFO] Running command: blastn -query GCF_000378205.1_ASM37820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95776166-4e77-44bc-86f9-b38b96454769/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378205.1_ASM37820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:05,113] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:05,117] [INFO] Selected 20 target genomes.
[2024-01-24 14:04:05,118] [INFO] Target genome list was writen to GCF_000378205.1_ASM37820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:05,160] [INFO] Task started: fastANI
[2024-01-24 14:04:05,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ae7f641-e3e5-4b9f-89d3-ac34f73643a4/GCF_000378205.1_ASM37820v1_genomic.fna.gz --refList GCF_000378205.1_ASM37820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378205.1_ASM37820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:15,318] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:15,324] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:15,324] [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_000378205.1	s__Sediminispirochaeta bajacaliforniensis	100.0	1475	1489	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000143985.1	s__Sediminispirochaeta smaragdinae	94.6108	1283	1489	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:15,327] [INFO] GTDB search result was written to GCF_000378205.1_ASM37820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:15,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:15,330] [INFO] DFAST_QC result json was written to GCF_000378205.1_ASM37820v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:15,330] [INFO] DFAST_QC completed!
[2024-01-24 14:04:15,330] [INFO] Total running time: 0h1m12s