[2024-01-24 12:21:57,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg0652aacf-cce7-4ab7-927b-e747c9f798dd/dqc_reference
[2024-01-24 12:21:58,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,939] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg66bd2010-b51e-418b-8548-46eae90bec62/GCF_000092405.1_ASM9240v1_genomic.fna.gz | prodigal -d GCF_000092405.1_ASM9240v1_genomic.fna/cds.fna -a GCF_000092405.1_ASM9240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:05,235] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:05,235] [INFO] Task started: HMMsearch
[2024-01-24 12:22:05,235] [INFO] Running command: hmmsearch --tblout GCF_000092405.1_ASM9240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0652aacf-cce7-4ab7-927b-e747c9f798dd/dqc_reference/reference_markers.hmm GCF_000092405.1_ASM9240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:05,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:05,502] [INFO] Found 6/6 markers.
[2024-01-24 12:22:05,541] [INFO] Query marker FASTA was written to GCF_000092405.1_ASM9240v1_genomic.fna/markers.fasta
[2024-01-24 12:22:05,541] [INFO] Task started: Blastn
[2024-01-24 12:22:05,541] [INFO] Running command: blastn -query GCF_000092405.1_ASM9240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0652aacf-cce7-4ab7-927b-e747c9f798dd/dqc_reference/reference_markers.fasta -out GCF_000092405.1_ASM9240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:06,254] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:06,258] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:06,258] [INFO] Target genome list was writen to GCF_000092405.1_ASM9240v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:06,262] [INFO] Task started: fastANI
[2024-01-24 12:22:06,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg66bd2010-b51e-418b-8548-46eae90bec62/GCF_000092405.1_ASM9240v1_genomic.fna.gz --refList GCF_000092405.1_ASM9240v1_genomic.fna/target_genomes.txt --output GCF_000092405.1_ASM9240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:13,131] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:13,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0652aacf-cce7-4ab7-927b-e747c9f798dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:13,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0652aacf-cce7-4ab7-927b-e747c9f798dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:13,135] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:13,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:13,135] [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
Syntrophothermus lipocalidus	strain=DSM 12680	GCA_000092405.1	86170	86170	type	True	100.0	801	801	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:22:13,138] [INFO] DFAST Taxonomy check result was written to GCF_000092405.1_ASM9240v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:13,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:13,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:13,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0652aacf-cce7-4ab7-927b-e747c9f798dd/dqc_reference/checkm_data
[2024-01-24 12:22:13,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:13,185] [INFO] Task started: CheckM
[2024-01-24 12:22:13,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092405.1_ASM9240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092405.1_ASM9240v1_genomic.fna/checkm_input GCF_000092405.1_ASM9240v1_genomic.fna/checkm_result
[2024-01-24 12:22:39,273] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:39,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:39,292] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:39,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:39,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092405.1_ASM9240v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:39,293] [INFO] Task started: Blastn
[2024-01-24 12:22:39,293] [INFO] Running command: blastn -query GCF_000092405.1_ASM9240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0652aacf-cce7-4ab7-927b-e747c9f798dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092405.1_ASM9240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:40,091] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:40,095] [INFO] Selected 13 target genomes.
[2024-01-24 12:22:40,095] [INFO] Target genome list was writen to GCF_000092405.1_ASM9240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:40,107] [INFO] Task started: fastANI
[2024-01-24 12:22:40,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg66bd2010-b51e-418b-8548-46eae90bec62/GCF_000092405.1_ASM9240v1_genomic.fna.gz --refList GCF_000092405.1_ASM9240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092405.1_ASM9240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:46,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:46,892] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:46,892] [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_000092405.1	s__Syntrophothermus lipocalidus	100.0	801	801	d__Bacteria;p__Firmicutes_B;c__Syntrophomonadia;o__Syntrophomonadales;f__Syntrophothermaceae;g__Syntrophothermus	95.0	98.15	97.57	0.89	0.84	3	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:22:46,894] [INFO] GTDB search result was written to GCF_000092405.1_ASM9240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:46,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:46,897] [INFO] DFAST_QC result json was written to GCF_000092405.1_ASM9240v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:46,897] [INFO] DFAST_QC completed!
[2024-01-24 12:22:46,897] [INFO] Total running time: 0h0m49s