[2023-06-29 04:25:04,391] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:25:04,395] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:25:04,395] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4c351e4-5e06-4d46-93e5-3e26c4021cb9/dqc_reference
[2023-06-29 04:25:05,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:25:05,692] [INFO] Task started: Prodigal
[2023-06-29 04:25:05,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bde15e2-ea6a-49cd-8e94-cd0061ff546a/GCA_015066045.1_ASM1506604v1_genomic.fna.gz | prodigal -d GCA_015066045.1_ASM1506604v1_genomic.fna/cds.fna -a GCA_015066045.1_ASM1506604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:25:10,191] [INFO] Task succeeded: Prodigal
[2023-06-29 04:25:10,192] [INFO] Task started: HMMsearch
[2023-06-29 04:25:10,192] [INFO] Running command: hmmsearch --tblout GCA_015066045.1_ASM1506604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4c351e4-5e06-4d46-93e5-3e26c4021cb9/dqc_reference/reference_markers.hmm GCA_015066045.1_ASM1506604v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:25:10,439] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:25:10,441] [INFO] Found 6/6 markers.
[2023-06-29 04:25:10,471] [INFO] Query marker FASTA was written to GCA_015066045.1_ASM1506604v1_genomic.fna/markers.fasta
[2023-06-29 04:25:10,472] [INFO] Task started: Blastn
[2023-06-29 04:25:10,472] [INFO] Running command: blastn -query GCA_015066045.1_ASM1506604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c351e4-5e06-4d46-93e5-3e26c4021cb9/dqc_reference/reference_markers.fasta -out GCA_015066045.1_ASM1506604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:25:11,101] [INFO] Task succeeded: Blastn
[2023-06-29 04:25:11,106] [INFO] Selected 21 target genomes.
[2023-06-29 04:25:11,107] [INFO] Target genome list was writen to GCA_015066045.1_ASM1506604v1_genomic.fna/target_genomes.txt
[2023-06-29 04:25:11,110] [INFO] Task started: fastANI
[2023-06-29 04:25:11,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bde15e2-ea6a-49cd-8e94-cd0061ff546a/GCA_015066045.1_ASM1506604v1_genomic.fna.gz --refList GCA_015066045.1_ASM1506604v1_genomic.fna/target_genomes.txt --output GCA_015066045.1_ASM1506604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:25:23,124] [INFO] Task succeeded: fastANI
[2023-06-29 04:25:23,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4c351e4-5e06-4d46-93e5-3e26c4021cb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:25:23,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4c351e4-5e06-4d46-93e5-3e26c4021cb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:25:23,127] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:25:23,127] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 04:25:23,127] [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
--------------------------------------------------------------------------------
[2023-06-29 04:25:23,129] [INFO] DFAST Taxonomy check result was written to GCA_015066045.1_ASM1506604v1_genomic.fna/tc_result.tsv
[2023-06-29 04:25:23,130] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:25:23,130] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:25:23,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4c351e4-5e06-4d46-93e5-3e26c4021cb9/dqc_reference/checkm_data
[2023-06-29 04:25:23,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:25:23,161] [INFO] Task started: CheckM
[2023-06-29 04:25:23,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015066045.1_ASM1506604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015066045.1_ASM1506604v1_genomic.fna/checkm_input GCA_015066045.1_ASM1506604v1_genomic.fna/checkm_result
[2023-06-29 04:25:43,958] [INFO] Task succeeded: CheckM
[2023-06-29 04:25:43,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:25:43,983] [INFO] ===== Completeness check finished =====
[2023-06-29 04:25:43,984] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:25:43,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015066045.1_ASM1506604v1_genomic.fna/markers.fasta)
[2023-06-29 04:25:43,985] [INFO] Task started: Blastn
[2023-06-29 04:25:43,985] [INFO] Running command: blastn -query GCA_015066045.1_ASM1506604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c351e4-5e06-4d46-93e5-3e26c4021cb9/dqc_reference/reference_markers_gtdb.fasta -out GCA_015066045.1_ASM1506604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:25:45,026] [INFO] Task succeeded: Blastn
[2023-06-29 04:25:45,031] [INFO] Selected 12 target genomes.
[2023-06-29 04:25:45,031] [INFO] Target genome list was writen to GCA_015066045.1_ASM1506604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:25:45,032] [INFO] Task started: fastANI
[2023-06-29 04:25:45,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bde15e2-ea6a-49cd-8e94-cd0061ff546a/GCA_015066045.1_ASM1506604v1_genomic.fna.gz --refList GCA_015066045.1_ASM1506604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015066045.1_ASM1506604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:25:50,503] [INFO] Task succeeded: fastANI
[2023-06-29 04:25:50,517] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:25:50,518] [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_015066045.1	s__UBA6857 sp015066045	100.0	711	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	98.36	98.36	0.84	0.84	2	conclusive
GCA_017436375.1	s__UBA6857 sp017436375	83.8353	445	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017516315.1	s__UBA6857 sp017516315	83.4172	490	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397845.1	s__UBA6857 sp017397845	82.5465	472	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066105.1	s__UBA6857 sp015066105	79.1542	246	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555765.1	s__UBA6857 sp017555765	78.8012	219	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017425745.1	s__UBA6857 sp017425745	78.2379	164	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	97.95	97.95	0.76	0.76	2	-
GCA_017472225.1	s__UBA6857 sp017472225	78.2265	184	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768075.1	s__UBA6857 sp900768075	78.0989	191	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631745.1	s__UBA6857 sp017631745	77.7884	170	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:25:50,520] [INFO] GTDB search result was written to GCA_015066045.1_ASM1506604v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:25:50,520] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:25:50,524] [INFO] DFAST_QC result json was written to GCA_015066045.1_ASM1506604v1_genomic.fna/dqc_result.json
[2023-06-29 04:25:50,524] [INFO] DFAST_QC completed!
[2023-06-29 04:25:50,524] [INFO] Total running time: 0h0m46s