[2024-01-24 12:48:20,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:20,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:20,409] [INFO] DQC Reference Directory: /var/lib/cwl/stge126837a-d2dd-45e4-b549-2ef62fbaf4bb/dqc_reference
[2024-01-24 12:48:21,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:21,596] [INFO] Task started: Prodigal
[2024-01-24 12:48:21,596] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa24f69d-0339-485c-ac30-810d897872f2/GCF_029167365.1_ASM2916736v1_genomic.fna.gz | prodigal -d GCF_029167365.1_ASM2916736v1_genomic.fna/cds.fna -a GCF_029167365.1_ASM2916736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:25,189] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:25,189] [INFO] Task started: HMMsearch
[2024-01-24 12:48:25,190] [INFO] Running command: hmmsearch --tblout GCF_029167365.1_ASM2916736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge126837a-d2dd-45e4-b549-2ef62fbaf4bb/dqc_reference/reference_markers.hmm GCF_029167365.1_ASM2916736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:25,424] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:25,425] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfa24f69d-0339-485c-ac30-810d897872f2/GCF_029167365.1_ASM2916736v1_genomic.fna.gz]
[2024-01-24 12:48:25,444] [INFO] Query marker FASTA was written to GCF_029167365.1_ASM2916736v1_genomic.fna/markers.fasta
[2024-01-24 12:48:25,445] [INFO] Task started: Blastn
[2024-01-24 12:48:25,445] [INFO] Running command: blastn -query GCF_029167365.1_ASM2916736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge126837a-d2dd-45e4-b549-2ef62fbaf4bb/dqc_reference/reference_markers.fasta -out GCF_029167365.1_ASM2916736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:26,037] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:26,041] [INFO] Selected 18 target genomes.
[2024-01-24 12:48:26,041] [INFO] Target genome list was writen to GCF_029167365.1_ASM2916736v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:26,062] [INFO] Task started: fastANI
[2024-01-24 12:48:26,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa24f69d-0339-485c-ac30-810d897872f2/GCF_029167365.1_ASM2916736v1_genomic.fna.gz --refList GCF_029167365.1_ASM2916736v1_genomic.fna/target_genomes.txt --output GCF_029167365.1_ASM2916736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:34,429] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:34,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge126837a-d2dd-45e4-b549-2ef62fbaf4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:34,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge126837a-d2dd-45e4-b549-2ef62fbaf4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:34,432] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:48:34,432] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 12:48:34,432] [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
--------------------------------------------------------------------------------
[2024-01-24 12:48:34,435] [INFO] DFAST Taxonomy check result was written to GCF_029167365.1_ASM2916736v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:34,436] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:34,436] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:34,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge126837a-d2dd-45e4-b549-2ef62fbaf4bb/dqc_reference/checkm_data
[2024-01-24 12:48:34,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:34,462] [INFO] Task started: CheckM
[2024-01-24 12:48:34,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029167365.1_ASM2916736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029167365.1_ASM2916736v1_genomic.fna/checkm_input GCF_029167365.1_ASM2916736v1_genomic.fna/checkm_result
[2024-01-24 12:48:52,835] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:52,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:52,859] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:52,859] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:52,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029167365.1_ASM2916736v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:52,860] [INFO] Task started: Blastn
[2024-01-24 12:48:52,860] [INFO] Running command: blastn -query GCF_029167365.1_ASM2916736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge126837a-d2dd-45e4-b549-2ef62fbaf4bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_029167365.1_ASM2916736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:53,702] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:53,707] [INFO] Selected 25 target genomes.
[2024-01-24 12:48:53,707] [INFO] Target genome list was writen to GCF_029167365.1_ASM2916736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:53,734] [INFO] Task started: fastANI
[2024-01-24 12:48:53,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa24f69d-0339-485c-ac30-810d897872f2/GCF_029167365.1_ASM2916736v1_genomic.fna.gz --refList GCF_029167365.1_ASM2916736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029167365.1_ASM2916736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:03,684] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:03,691] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:03,691] [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
GCA_001552885.1	s__KA00274 sp001552885	99.9532	499	537	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Fastidiosipilaceae;g__KA00274	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902373515.1	s__KA00274 sp902373515	78.3616	76	537	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Fastidiosipilaceae;g__KA00274	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:03,693] [INFO] GTDB search result was written to GCF_029167365.1_ASM2916736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:03,693] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:03,696] [INFO] DFAST_QC result json was written to GCF_029167365.1_ASM2916736v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:03,696] [INFO] DFAST_QC completed!
[2024-01-24 12:49:03,696] [INFO] Total running time: 0h0m43s