[2023-06-05 01:18:09,331] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:18:09,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:18:09,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fe462e0-c8e9-4526-8235-3aa684d00d25/dqc_reference
[2023-06-05 01:18:11,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:11,692] [INFO] Task started: Prodigal
[2023-06-05 01:18:11,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd161535-547a-4ed9-b385-70463a3ecf08/GCA_934458775.1_ERR7738171_bin.41_genomic.fna.gz | prodigal -d GCA_934458775.1_ERR7738171_bin.41_genomic.fna/cds.fna -a GCA_934458775.1_ERR7738171_bin.41_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:18,082] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:18,083] [INFO] Task started: HMMsearch
[2023-06-05 01:18:18,083] [INFO] Running command: hmmsearch --tblout GCA_934458775.1_ERR7738171_bin.41_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fe462e0-c8e9-4526-8235-3aa684d00d25/dqc_reference/reference_markers.hmm GCA_934458775.1_ERR7738171_bin.41_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:18,369] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:18,371] [INFO] Found 6/6 markers.
[2023-06-05 01:18:18,402] [INFO] Query marker FASTA was written to GCA_934458775.1_ERR7738171_bin.41_genomic.fna/markers.fasta
[2023-06-05 01:18:18,403] [INFO] Task started: Blastn
[2023-06-05 01:18:18,403] [INFO] Running command: blastn -query GCA_934458775.1_ERR7738171_bin.41_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fe462e0-c8e9-4526-8235-3aa684d00d25/dqc_reference/reference_markers.fasta -out GCA_934458775.1_ERR7738171_bin.41_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:19,056] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:19,060] [INFO] Selected 25 target genomes.
[2023-06-05 01:18:19,060] [INFO] Target genome list was writen to GCA_934458775.1_ERR7738171_bin.41_genomic.fna/target_genomes.txt
[2023-06-05 01:18:19,102] [INFO] Task started: fastANI
[2023-06-05 01:18:19,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd161535-547a-4ed9-b385-70463a3ecf08/GCA_934458775.1_ERR7738171_bin.41_genomic.fna.gz --refList GCA_934458775.1_ERR7738171_bin.41_genomic.fna/target_genomes.txt --output GCA_934458775.1_ERR7738171_bin.41_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:32,863] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:32,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fe462e0-c8e9-4526-8235-3aa684d00d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:32,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fe462e0-c8e9-4526-8235-3aa684d00d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:32,865] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:32,865] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:18:32,865] [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
--------------------------------------------------------------------------------
[2023-06-05 01:18:32,867] [INFO] DFAST Taxonomy check result was written to GCA_934458775.1_ERR7738171_bin.41_genomic.fna/tc_result.tsv
[2023-06-05 01:18:32,867] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:32,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:32,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fe462e0-c8e9-4526-8235-3aa684d00d25/dqc_reference/checkm_data
[2023-06-05 01:18:32,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:32,903] [INFO] Task started: CheckM
[2023-06-05 01:18:32,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934458775.1_ERR7738171_bin.41_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934458775.1_ERR7738171_bin.41_genomic.fna/checkm_input GCA_934458775.1_ERR7738171_bin.41_genomic.fna/checkm_result
[2023-06-05 01:18:57,765] [INFO] Task succeeded: CheckM
[2023-06-05 01:18:57,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:18:57,788] [INFO] ===== Completeness check finished =====
[2023-06-05 01:18:57,788] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:18:57,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934458775.1_ERR7738171_bin.41_genomic.fna/markers.fasta)
[2023-06-05 01:18:57,789] [INFO] Task started: Blastn
[2023-06-05 01:18:57,789] [INFO] Running command: blastn -query GCA_934458775.1_ERR7738171_bin.41_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fe462e0-c8e9-4526-8235-3aa684d00d25/dqc_reference/reference_markers_gtdb.fasta -out GCA_934458775.1_ERR7738171_bin.41_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:58,888] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:58,893] [INFO] Selected 10 target genomes.
[2023-06-05 01:18:58,894] [INFO] Target genome list was writen to GCA_934458775.1_ERR7738171_bin.41_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:18:58,902] [INFO] Task started: fastANI
[2023-06-05 01:18:58,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd161535-547a-4ed9-b385-70463a3ecf08/GCA_934458775.1_ERR7738171_bin.41_genomic.fna.gz --refList GCA_934458775.1_ERR7738171_bin.41_genomic.fna/target_genomes_gtdb.txt --output GCA_934458775.1_ERR7738171_bin.41_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:19:04,915] [INFO] Task succeeded: fastANI
[2023-06-05 01:19:04,928] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:19:04,929] [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_000432175.1	s__CAG-115 sp000432175	97.2677	648	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.02	98.02	0.85	0.84	3	conclusive
GCA_900542145.1	s__CAG-115 sp003507295	84.3685	543	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.16	97.02	0.91	0.87	5	-
GCA_900768125.1	s__CAG-115 sp900768125	83.0793	472	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.01	98.01	0.87	0.87	2	-
GCA_003531585.1	s__CAG-115 sp003531585	82.9333	455	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.38	98.23	0.90	0.86	9	-
GCA_017829075.1	s__CAG-115 sp017829075	80.78	425	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465665.1	s__CAG-115 sp017465665	78.0238	161	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848155.1	s__CAG-115 sp017848155	77.7273	121	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799395.1	s__CAG-115 sp014799395	77.3415	159	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017440445.1	s__CAG-115 sp017440445	77.0083	110	837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:19:04,930] [INFO] GTDB search result was written to GCA_934458775.1_ERR7738171_bin.41_genomic.fna/result_gtdb.tsv
[2023-06-05 01:19:04,931] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:19:04,934] [INFO] DFAST_QC result json was written to GCA_934458775.1_ERR7738171_bin.41_genomic.fna/dqc_result.json
[2023-06-05 01:19:04,934] [INFO] DFAST_QC completed!
[2023-06-05 01:19:04,934] [INFO] Total running time: 0h0m56s