[2024-01-24 14:05:15,143] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:15,145] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:15,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b993322-98a8-417d-a4aa-8a0f2ff784c3/dqc_reference
[2024-01-24 14:05:16,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:16,330] [INFO] Task started: Prodigal
[2024-01-24 14:05:16,331] [INFO] Running command: gunzip -c /var/lib/cwl/stgda6bd1ff-2257-4c78-b027-51db7fa340be/GCF_014207565.1_ASM1420756v1_genomic.fna.gz | prodigal -d GCF_014207565.1_ASM1420756v1_genomic.fna/cds.fna -a GCF_014207565.1_ASM1420756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:27,242] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:27,243] [INFO] Task started: HMMsearch
[2024-01-24 14:05:27,243] [INFO] Running command: hmmsearch --tblout GCF_014207565.1_ASM1420756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b993322-98a8-417d-a4aa-8a0f2ff784c3/dqc_reference/reference_markers.hmm GCF_014207565.1_ASM1420756v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:27,541] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:27,542] [INFO] Found 6/6 markers.
[2024-01-24 14:05:27,587] [INFO] Query marker FASTA was written to GCF_014207565.1_ASM1420756v1_genomic.fna/markers.fasta
[2024-01-24 14:05:27,587] [INFO] Task started: Blastn
[2024-01-24 14:05:27,587] [INFO] Running command: blastn -query GCF_014207565.1_ASM1420756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b993322-98a8-417d-a4aa-8a0f2ff784c3/dqc_reference/reference_markers.fasta -out GCF_014207565.1_ASM1420756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:28,147] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:28,151] [INFO] Selected 15 target genomes.
[2024-01-24 14:05:28,152] [INFO] Target genome list was writen to GCF_014207565.1_ASM1420756v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:28,182] [INFO] Task started: fastANI
[2024-01-24 14:05:28,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgda6bd1ff-2257-4c78-b027-51db7fa340be/GCF_014207565.1_ASM1420756v1_genomic.fna.gz --refList GCF_014207565.1_ASM1420756v1_genomic.fna/target_genomes.txt --output GCF_014207565.1_ASM1420756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:36,003] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:36,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b993322-98a8-417d-a4aa-8a0f2ff784c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:36,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b993322-98a8-417d-a4aa-8a0f2ff784c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:36,010] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:36,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:36,010] [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
Spirochaeta isovalerica	strain=DSM 2461	GCA_014207565.1	150	150	type	True	100.0	1602	1606	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:05:36,011] [INFO] DFAST Taxonomy check result was written to GCF_014207565.1_ASM1420756v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:36,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:36,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:36,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b993322-98a8-417d-a4aa-8a0f2ff784c3/dqc_reference/checkm_data
[2024-01-24 14:05:36,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:36,063] [INFO] Task started: CheckM
[2024-01-24 14:05:36,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207565.1_ASM1420756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207565.1_ASM1420756v1_genomic.fna/checkm_input GCF_014207565.1_ASM1420756v1_genomic.fna/checkm_result
[2024-01-24 14:06:13,712] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:13,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:13,732] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:13,733] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:13,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207565.1_ASM1420756v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:13,734] [INFO] Task started: Blastn
[2024-01-24 14:06:13,734] [INFO] Running command: blastn -query GCF_014207565.1_ASM1420756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b993322-98a8-417d-a4aa-8a0f2ff784c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207565.1_ASM1420756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:14,694] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:14,698] [INFO] Selected 20 target genomes.
[2024-01-24 14:06:14,698] [INFO] Target genome list was writen to GCF_014207565.1_ASM1420756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:14,723] [INFO] Task started: fastANI
[2024-01-24 14:06:14,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgda6bd1ff-2257-4c78-b027-51db7fa340be/GCF_014207565.1_ASM1420756v1_genomic.fna.gz --refList GCF_014207565.1_ASM1420756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207565.1_ASM1420756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:28,208] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:28,213] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:28,214] [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_014207565.1	s__Spirochaeta_F isovalerica	100.0	1603	1606	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Spirochaeta_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016936555.1	s__Spirochaeta_F sp016936555	82.7468	937	1606	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Spirochaeta_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342385.1	s__Spirochaeta_F sp016342385	77.006	151	1606	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Spirochaeta_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744925.1	s__Spirochaeta_F sp016744925	76.5933	174	1606	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Spirochaeta_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:28,215] [INFO] GTDB search result was written to GCF_014207565.1_ASM1420756v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:28,216] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:28,218] [INFO] DFAST_QC result json was written to GCF_014207565.1_ASM1420756v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:28,218] [INFO] DFAST_QC completed!
[2024-01-24 14:06:28,218] [INFO] Total running time: 0h1m13s