[2023-06-13 22:22:02,263] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:22:02,266] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:22:02,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg904d52a0-1979-411e-ba42-21fc90898bc8/dqc_reference
[2023-06-13 22:22:03,510] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:22:03,511] [INFO] Task started: Prodigal
[2023-06-13 22:22:03,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg2eb1f98e-85c0-4a27-aa51-a3ab3f763a58/GCA_022448265.1_ASM2244826v1_genomic.fna.gz | prodigal -d GCA_022448265.1_ASM2244826v1_genomic.fna/cds.fna -a GCA_022448265.1_ASM2244826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:22:14,376] [INFO] Task succeeded: Prodigal
[2023-06-13 22:22:14,376] [INFO] Task started: HMMsearch
[2023-06-13 22:22:14,377] [INFO] Running command: hmmsearch --tblout GCA_022448265.1_ASM2244826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg904d52a0-1979-411e-ba42-21fc90898bc8/dqc_reference/reference_markers.hmm GCA_022448265.1_ASM2244826v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:22:14,601] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:22:14,602] [INFO] Found 6/6 markers.
[2023-06-13 22:22:14,630] [INFO] Query marker FASTA was written to GCA_022448265.1_ASM2244826v1_genomic.fna/markers.fasta
[2023-06-13 22:22:14,631] [INFO] Task started: Blastn
[2023-06-13 22:22:14,631] [INFO] Running command: blastn -query GCA_022448265.1_ASM2244826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg904d52a0-1979-411e-ba42-21fc90898bc8/dqc_reference/reference_markers.fasta -out GCA_022448265.1_ASM2244826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:22:15,199] [INFO] Task succeeded: Blastn
[2023-06-13 22:22:15,203] [INFO] Selected 21 target genomes.
[2023-06-13 22:22:15,204] [INFO] Target genome list was writen to GCA_022448265.1_ASM2244826v1_genomic.fna/target_genomes.txt
[2023-06-13 22:22:15,206] [INFO] Task started: fastANI
[2023-06-13 22:22:15,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb1f98e-85c0-4a27-aa51-a3ab3f763a58/GCA_022448265.1_ASM2244826v1_genomic.fna.gz --refList GCA_022448265.1_ASM2244826v1_genomic.fna/target_genomes.txt --output GCA_022448265.1_ASM2244826v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:22:30,872] [INFO] Task succeeded: fastANI
[2023-06-13 22:22:30,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg904d52a0-1979-411e-ba42-21fc90898bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:22:30,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg904d52a0-1979-411e-ba42-21fc90898bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:22:30,877] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:22:30,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:22:30,877] [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
Bythopirellula polymerisocia	strain=Pla144	GCA_007860015.1	2528003	2528003	type	True	76.7563	54	1167	95	below_threshold
Bythopirellula goksoeyrii	strain=Pr1d	GCA_008065115.1	1400387	1400387	type	True	76.301	56	1167	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:22:30,881] [INFO] DFAST Taxonomy check result was written to GCA_022448265.1_ASM2244826v1_genomic.fna/tc_result.tsv
[2023-06-13 22:22:30,881] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:22:30,881] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:22:30,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg904d52a0-1979-411e-ba42-21fc90898bc8/dqc_reference/checkm_data
[2023-06-13 22:22:30,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:22:30,924] [INFO] Task started: CheckM
[2023-06-13 22:22:30,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448265.1_ASM2244826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448265.1_ASM2244826v1_genomic.fna/checkm_input GCA_022448265.1_ASM2244826v1_genomic.fna/checkm_result
[2023-06-13 22:23:06,274] [INFO] Task succeeded: CheckM
[2023-06-13 22:23:06,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 22:23:06,302] [INFO] ===== Completeness check finished =====
[2023-06-13 22:23:06,302] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:23:06,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448265.1_ASM2244826v1_genomic.fna/markers.fasta)
[2023-06-13 22:23:06,303] [INFO] Task started: Blastn
[2023-06-13 22:23:06,303] [INFO] Running command: blastn -query GCA_022448265.1_ASM2244826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg904d52a0-1979-411e-ba42-21fc90898bc8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448265.1_ASM2244826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:23:07,058] [INFO] Task succeeded: Blastn
[2023-06-13 22:23:07,063] [INFO] Selected 18 target genomes.
[2023-06-13 22:23:07,063] [INFO] Target genome list was writen to GCA_022448265.1_ASM2244826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:23:07,067] [INFO] Task started: fastANI
[2023-06-13 22:23:07,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb1f98e-85c0-4a27-aa51-a3ab3f763a58/GCA_022448265.1_ASM2244826v1_genomic.fna.gz --refList GCA_022448265.1_ASM2244826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448265.1_ASM2244826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:23:20,420] [INFO] Task succeeded: fastANI
[2023-06-13 22:23:20,426] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:23:20,427] [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_007860015.1	s__Bythopirellula polymerisocia	76.7563	54	1167	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065115.1	s__Bythopirellula goksoyri	76.301	56	1167	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	76.1394	62	1167	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152205.1	s__Bythopirellula sp013152205	75.9692	65	1167	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152515.1	s__Bythopirellula sp013152515	75.8703	66	1167	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:23:20,429] [INFO] GTDB search result was written to GCA_022448265.1_ASM2244826v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:23:20,429] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:23:20,432] [INFO] DFAST_QC result json was written to GCA_022448265.1_ASM2244826v1_genomic.fna/dqc_result.json
[2023-06-13 22:23:20,432] [INFO] DFAST_QC completed!
[2023-06-13 22:23:20,432] [INFO] Total running time: 0h1m18s