[2023-06-28 03:25:03,445] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:25:03,447] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:25:03,447] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfb11dfc-bb10-4711-ba0b-9b8acc5c9a4d/dqc_reference
[2023-06-28 03:25:04,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:25:04,749] [INFO] Task started: Prodigal
[2023-06-28 03:25:04,749] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb8e753a-1141-4527-a0f2-f1380fb71e61/GCA_002708305.1_ASM270830v1_genomic.fna.gz | prodigal -d GCA_002708305.1_ASM270830v1_genomic.fna/cds.fna -a GCA_002708305.1_ASM270830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:25:11,743] [INFO] Task succeeded: Prodigal
[2023-06-28 03:25:11,744] [INFO] Task started: HMMsearch
[2023-06-28 03:25:11,744] [INFO] Running command: hmmsearch --tblout GCA_002708305.1_ASM270830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfb11dfc-bb10-4711-ba0b-9b8acc5c9a4d/dqc_reference/reference_markers.hmm GCA_002708305.1_ASM270830v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:25:12,003] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:25:12,004] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdb8e753a-1141-4527-a0f2-f1380fb71e61/GCA_002708305.1_ASM270830v1_genomic.fna.gz]
[2023-06-28 03:25:12,047] [INFO] Query marker FASTA was written to GCA_002708305.1_ASM270830v1_genomic.fna/markers.fasta
[2023-06-28 03:25:12,048] [INFO] Task started: Blastn
[2023-06-28 03:25:12,048] [INFO] Running command: blastn -query GCA_002708305.1_ASM270830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfb11dfc-bb10-4711-ba0b-9b8acc5c9a4d/dqc_reference/reference_markers.fasta -out GCA_002708305.1_ASM270830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:12,682] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:12,686] [INFO] Selected 14 target genomes.
[2023-06-28 03:25:12,687] [INFO] Target genome list was writen to GCA_002708305.1_ASM270830v1_genomic.fna/target_genomes.txt
[2023-06-28 03:25:12,689] [INFO] Task started: fastANI
[2023-06-28 03:25:12,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8e753a-1141-4527-a0f2-f1380fb71e61/GCA_002708305.1_ASM270830v1_genomic.fna.gz --refList GCA_002708305.1_ASM270830v1_genomic.fna/target_genomes.txt --output GCA_002708305.1_ASM270830v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:25:18,906] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:18,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfb11dfc-bb10-4711-ba0b-9b8acc5c9a4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:25:18,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfb11dfc-bb10-4711-ba0b-9b8acc5c9a4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:25:18,908] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:25:18,908] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 03:25:18,908] [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
--------------------------------------------------------------------------------
[2023-06-28 03:25:18,910] [INFO] DFAST Taxonomy check result was written to GCA_002708305.1_ASM270830v1_genomic.fna/tc_result.tsv
[2023-06-28 03:25:18,911] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:25:18,911] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:25:18,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfb11dfc-bb10-4711-ba0b-9b8acc5c9a4d/dqc_reference/checkm_data
[2023-06-28 03:25:18,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:25:18,952] [INFO] Task started: CheckM
[2023-06-28 03:25:18,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708305.1_ASM270830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708305.1_ASM270830v1_genomic.fna/checkm_input GCA_002708305.1_ASM270830v1_genomic.fna/checkm_result
[2023-06-28 03:25:46,765] [INFO] Task succeeded: CheckM
[2023-06-28 03:25:46,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:25:46,787] [INFO] ===== Completeness check finished =====
[2023-06-28 03:25:46,788] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:25:46,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708305.1_ASM270830v1_genomic.fna/markers.fasta)
[2023-06-28 03:25:46,788] [INFO] Task started: Blastn
[2023-06-28 03:25:46,789] [INFO] Running command: blastn -query GCA_002708305.1_ASM270830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfb11dfc-bb10-4711-ba0b-9b8acc5c9a4d/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708305.1_ASM270830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:47,663] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:47,667] [INFO] Selected 19 target genomes.
[2023-06-28 03:25:47,667] [INFO] Target genome list was writen to GCA_002708305.1_ASM270830v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:25:47,678] [INFO] Task started: fastANI
[2023-06-28 03:25:47,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8e753a-1141-4527-a0f2-f1380fb71e61/GCA_002708305.1_ASM270830v1_genomic.fna.gz --refList GCA_002708305.1_ASM270830v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708305.1_ASM270830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:25:53,153] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:53,158] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 03:25:53,158] [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_002708305.1	s__UBA7326 sp002708305	100.0	1049	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	98.40	98.02	0.79	0.75	5	conclusive
GCA_003284265.1	s__UBA7326 sp003284265	77.9064	172	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002709155.1	s__UBA7326 sp002709155	76.8275	123	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:25:53,160] [INFO] GTDB search result was written to GCA_002708305.1_ASM270830v1_genomic.fna/result_gtdb.tsv
[2023-06-28 03:25:53,161] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:25:53,177] [INFO] DFAST_QC result json was written to GCA_002708305.1_ASM270830v1_genomic.fna/dqc_result.json
[2023-06-28 03:25:53,178] [INFO] DFAST_QC completed!
[2023-06-28 03:25:53,178] [INFO] Total running time: 0h0m50s