[2024-01-25 19:59:20,477] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:20,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:20,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg2224605a-d735-47cf-9984-53309fb3a51a/dqc_reference
[2024-01-25 19:59:21,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:21,686] [INFO] Task started: Prodigal
[2024-01-25 19:59:21,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg5200a5b8-fd03-41b9-9573-50ad95279ac6/GCF_024172705.1_ASM2417270v1_genomic.fna.gz | prodigal -d GCF_024172705.1_ASM2417270v1_genomic.fna/cds.fna -a GCF_024172705.1_ASM2417270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:23,517] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:23,517] [INFO] Task started: HMMsearch
[2024-01-25 19:59:23,517] [INFO] Running command: hmmsearch --tblout GCF_024172705.1_ASM2417270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2224605a-d735-47cf-9984-53309fb3a51a/dqc_reference/reference_markers.hmm GCF_024172705.1_ASM2417270v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:23,696] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:23,697] [INFO] Found 6/6 markers.
[2024-01-25 19:59:23,710] [INFO] Query marker FASTA was written to GCF_024172705.1_ASM2417270v1_genomic.fna/markers.fasta
[2024-01-25 19:59:23,711] [INFO] Task started: Blastn
[2024-01-25 19:59:23,711] [INFO] Running command: blastn -query GCF_024172705.1_ASM2417270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2224605a-d735-47cf-9984-53309fb3a51a/dqc_reference/reference_markers.fasta -out GCF_024172705.1_ASM2417270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:24,290] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:24,292] [INFO] Selected 23 target genomes.
[2024-01-25 19:59:24,293] [INFO] Target genome list was writen to GCF_024172705.1_ASM2417270v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:24,301] [INFO] Task started: fastANI
[2024-01-25 19:59:24,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg5200a5b8-fd03-41b9-9573-50ad95279ac6/GCF_024172705.1_ASM2417270v1_genomic.fna.gz --refList GCF_024172705.1_ASM2417270v1_genomic.fna/target_genomes.txt --output GCF_024172705.1_ASM2417270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:32,940] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:32,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2224605a-d735-47cf-9984-53309fb3a51a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:32,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2224605a-d735-47cf-9984-53309fb3a51a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:32,944] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:32,944] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:32,944] [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
Candidatus Comchoanobacter bicostacola	strain=Comchoano-1	GCA_024172705.1	2919598	2919598	type	True	100.0	335	335	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:59:32,945] [INFO] DFAST Taxonomy check result was written to GCF_024172705.1_ASM2417270v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:32,946] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:32,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:32,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2224605a-d735-47cf-9984-53309fb3a51a/dqc_reference/checkm_data
[2024-01-25 19:59:32,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:32,959] [INFO] Task started: CheckM
[2024-01-25 19:59:32,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024172705.1_ASM2417270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024172705.1_ASM2417270v1_genomic.fna/checkm_input GCF_024172705.1_ASM2417270v1_genomic.fna/checkm_result
[2024-01-25 19:59:45,733] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:45,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:45,750] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:45,750] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:45,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024172705.1_ASM2417270v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:45,750] [INFO] Task started: Blastn
[2024-01-25 19:59:45,750] [INFO] Running command: blastn -query GCF_024172705.1_ASM2417270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2224605a-d735-47cf-9984-53309fb3a51a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024172705.1_ASM2417270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:46,697] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:46,700] [INFO] Selected 30 target genomes.
[2024-01-25 19:59:46,700] [INFO] Target genome list was writen to GCF_024172705.1_ASM2417270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:46,732] [INFO] Task started: fastANI
[2024-01-25 19:59:46,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg5200a5b8-fd03-41b9-9573-50ad95279ac6/GCF_024172705.1_ASM2417270v1_genomic.fna.gz --refList GCF_024172705.1_ASM2417270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024172705.1_ASM2417270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:01,726] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:01,728] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:00:01,728] [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
--------------------------------------------------------------------------------
[2024-01-25 20:00:01,729] [INFO] GTDB search result was written to GCF_024172705.1_ASM2417270v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:01,730] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:01,731] [INFO] DFAST_QC result json was written to GCF_024172705.1_ASM2417270v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:01,731] [INFO] DFAST_QC completed!
[2024-01-25 20:00:01,731] [INFO] Total running time: 0h0m41s