[2024-01-24 15:32:05,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ea231ae-f6cb-42e1-a904-d591714f59b6/dqc_reference
[2024-01-24 15:32:06,985] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:06,986] [INFO] Task started: Prodigal
[2024-01-24 15:32:06,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c80ff64-96b1-45c4-abc6-10f7746b492b/GCF_011059145.1_ASM1105914v1_genomic.fna.gz | prodigal -d GCF_011059145.1_ASM1105914v1_genomic.fna/cds.fna -a GCF_011059145.1_ASM1105914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:23,759] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:23,760] [INFO] Task started: HMMsearch
[2024-01-24 15:32:23,760] [INFO] Running command: hmmsearch --tblout GCF_011059145.1_ASM1105914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ea231ae-f6cb-42e1-a904-d591714f59b6/dqc_reference/reference_markers.hmm GCF_011059145.1_ASM1105914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:24,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:24,057] [INFO] Found 6/6 markers.
[2024-01-24 15:32:24,092] [INFO] Query marker FASTA was written to GCF_011059145.1_ASM1105914v1_genomic.fna/markers.fasta
[2024-01-24 15:32:24,093] [INFO] Task started: Blastn
[2024-01-24 15:32:24,093] [INFO] Running command: blastn -query GCF_011059145.1_ASM1105914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ea231ae-f6cb-42e1-a904-d591714f59b6/dqc_reference/reference_markers.fasta -out GCF_011059145.1_ASM1105914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:24,677] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:24,682] [INFO] Selected 16 target genomes.
[2024-01-24 15:32:24,682] [INFO] Target genome list was writen to GCF_011059145.1_ASM1105914v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:24,696] [INFO] Task started: fastANI
[2024-01-24 15:32:24,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c80ff64-96b1-45c4-abc6-10f7746b492b/GCF_011059145.1_ASM1105914v1_genomic.fna.gz --refList GCF_011059145.1_ASM1105914v1_genomic.fna/target_genomes.txt --output GCF_011059145.1_ASM1105914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:36,071] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:36,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ea231ae-f6cb-42e1-a904-d591714f59b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:36,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ea231ae-f6cb-42e1-a904-d591714f59b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:36,081] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:36,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:36,082] [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
Halalkalibaculum roseum	strain=YR4-1	GCA_011059145.1	2709311	2709311	type	True	100.0	1266	1266	95	conclusive
Aliifodinibius halophilus	strain=2W32	GCA_011059105.1	1736908	1736908	type	True	76.2446	66	1266	95	below_threshold
Aliifodinibius saliphilus	strain=ECH52	GCA_005869845.1	1920650	1920650	type	True	76.0861	65	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:36,083] [INFO] DFAST Taxonomy check result was written to GCF_011059145.1_ASM1105914v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:36,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:36,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:36,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ea231ae-f6cb-42e1-a904-d591714f59b6/dqc_reference/checkm_data
[2024-01-24 15:32:36,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:36,126] [INFO] Task started: CheckM
[2024-01-24 15:32:36,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011059145.1_ASM1105914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011059145.1_ASM1105914v1_genomic.fna/checkm_input GCF_011059145.1_ASM1105914v1_genomic.fna/checkm_result
[2024-01-24 15:33:27,155] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:27,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:27,180] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:27,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:27,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011059145.1_ASM1105914v1_genomic.fna/markers.fasta)
[2024-01-24 15:33:27,182] [INFO] Task started: Blastn
[2024-01-24 15:33:27,182] [INFO] Running command: blastn -query GCF_011059145.1_ASM1105914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ea231ae-f6cb-42e1-a904-d591714f59b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_011059145.1_ASM1105914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:33:28,030] [INFO] Task succeeded: Blastn
[2024-01-24 15:33:28,034] [INFO] Selected 22 target genomes.
[2024-01-24 15:33:28,035] [INFO] Target genome list was writen to GCF_011059145.1_ASM1105914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:33:28,072] [INFO] Task started: fastANI
[2024-01-24 15:33:28,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c80ff64-96b1-45c4-abc6-10f7746b492b/GCF_011059145.1_ASM1105914v1_genomic.fna.gz --refList GCF_011059145.1_ASM1105914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011059145.1_ASM1105914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:33:41,574] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:41,581] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:33:41,581] [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_011059145.1	s__YR4-1 sp011059145	100.0	1266	1266	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__YR4-1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011059105.1	s__Fodinibius halophilus	76.2446	66	1266	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869845.1	s__Fodinibius saliphilus	76.0861	65	1266	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:33:41,583] [INFO] GTDB search result was written to GCF_011059145.1_ASM1105914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:33:41,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:33:41,586] [INFO] DFAST_QC result json was written to GCF_011059145.1_ASM1105914v1_genomic.fna/dqc_result.json
[2024-01-24 15:33:41,586] [INFO] DFAST_QC completed!
[2024-01-24 15:33:41,586] [INFO] Total running time: 0h1m36s