[2023-06-17 14:48:55,712] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:48:55,718] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:48:55,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e594c7b-4c41-4d45-9e71-b517cc8080b5/dqc_reference
[2023-06-17 14:48:56,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:48:56,968] [INFO] Task started: Prodigal
[2023-06-17 14:48:56,972] [INFO] Running command: gunzip -c /var/lib/cwl/stg10e4f5bd-b0c2-433c-ac8b-373a552b69a8/GCA_003671175.1_ASM367117v1_genomic.fna.gz | prodigal -d GCA_003671175.1_ASM367117v1_genomic.fna/cds.fna -a GCA_003671175.1_ASM367117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:49:04,991] [INFO] Task succeeded: Prodigal
[2023-06-17 14:49:04,991] [INFO] Task started: HMMsearch
[2023-06-17 14:49:04,991] [INFO] Running command: hmmsearch --tblout GCA_003671175.1_ASM367117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e594c7b-4c41-4d45-9e71-b517cc8080b5/dqc_reference/reference_markers.hmm GCA_003671175.1_ASM367117v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:49:05,255] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:49:05,257] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg10e4f5bd-b0c2-433c-ac8b-373a552b69a8/GCA_003671175.1_ASM367117v1_genomic.fna.gz]
[2023-06-17 14:49:05,293] [INFO] Query marker FASTA was written to GCA_003671175.1_ASM367117v1_genomic.fna/markers.fasta
[2023-06-17 14:49:05,294] [INFO] Task started: Blastn
[2023-06-17 14:49:05,294] [INFO] Running command: blastn -query GCA_003671175.1_ASM367117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e594c7b-4c41-4d45-9e71-b517cc8080b5/dqc_reference/reference_markers.fasta -out GCA_003671175.1_ASM367117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:49:05,915] [INFO] Task succeeded: Blastn
[2023-06-17 14:49:05,919] [INFO] Selected 12 target genomes.
[2023-06-17 14:49:05,919] [INFO] Target genome list was writen to GCA_003671175.1_ASM367117v1_genomic.fna/target_genomes.txt
[2023-06-17 14:49:05,925] [INFO] Task started: fastANI
[2023-06-17 14:49:05,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e4f5bd-b0c2-433c-ac8b-373a552b69a8/GCA_003671175.1_ASM367117v1_genomic.fna.gz --refList GCA_003671175.1_ASM367117v1_genomic.fna/target_genomes.txt --output GCA_003671175.1_ASM367117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:49:16,869] [INFO] Task succeeded: fastANI
[2023-06-17 14:49:16,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e594c7b-4c41-4d45-9e71-b517cc8080b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:49:16,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e594c7b-4c41-4d45-9e71-b517cc8080b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:49:16,871] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:49:16,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:49:16,872] [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
--------------------------------------------------------------------------------
[2023-06-17 14:49:16,874] [INFO] DFAST Taxonomy check result was written to GCA_003671175.1_ASM367117v1_genomic.fna/tc_result.tsv
[2023-06-17 14:49:16,875] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:49:16,875] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:49:16,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e594c7b-4c41-4d45-9e71-b517cc8080b5/dqc_reference/checkm_data
[2023-06-17 14:49:16,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:49:16,913] [INFO] Task started: CheckM
[2023-06-17 14:49:16,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003671175.1_ASM367117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003671175.1_ASM367117v1_genomic.fna/checkm_input GCA_003671175.1_ASM367117v1_genomic.fna/checkm_result
[2023-06-17 14:49:47,092] [INFO] Task succeeded: CheckM
[2023-06-17 14:49:47,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:49:47,119] [INFO] ===== Completeness check finished =====
[2023-06-17 14:49:47,120] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:49:47,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003671175.1_ASM367117v1_genomic.fna/markers.fasta)
[2023-06-17 14:49:47,122] [INFO] Task started: Blastn
[2023-06-17 14:49:47,122] [INFO] Running command: blastn -query GCA_003671175.1_ASM367117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e594c7b-4c41-4d45-9e71-b517cc8080b5/dqc_reference/reference_markers_gtdb.fasta -out GCA_003671175.1_ASM367117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:49:47,981] [INFO] Task succeeded: Blastn
[2023-06-17 14:49:47,985] [INFO] Selected 16 target genomes.
[2023-06-17 14:49:47,986] [INFO] Target genome list was writen to GCA_003671175.1_ASM367117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:49:47,997] [INFO] Task started: fastANI
[2023-06-17 14:49:47,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e4f5bd-b0c2-433c-ac8b-373a552b69a8/GCA_003671175.1_ASM367117v1_genomic.fna.gz --refList GCA_003671175.1_ASM367117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003671175.1_ASM367117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:50:02,648] [INFO] Task succeeded: fastANI
[2023-06-17 14:50:02,658] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:50:02,658] [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_903904835.1	s__Schlesneria sp903904835	76.638	120	862	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	98.97	98.46	0.92	0.88	7	-
GCA_903899985.1	s__Schlesneria sp903899985	76.5887	118	862	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.71	99.71	0.95	0.95	2	-
GCA_903834925.1	s__Schlesneria sp903834925	76.5451	129	862	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.97	99.97	0.97	0.97	2	-
GCA_903871875.1	s__Schlesneria sp903871875	76.5088	107	862	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.94	99.93	0.97	0.97	4	-
GCF_000255655.1	s__Schlesneria paludicola	76.1208	88	862	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:50:02,660] [INFO] GTDB search result was written to GCA_003671175.1_ASM367117v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:50:02,660] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:50:02,663] [INFO] DFAST_QC result json was written to GCA_003671175.1_ASM367117v1_genomic.fna/dqc_result.json
[2023-06-17 14:50:02,663] [INFO] DFAST_QC completed!
[2023-06-17 14:50:02,663] [INFO] Total running time: 0h1m7s