[2023-06-13 14:58:38,687] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:58:38,690] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:58:38,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg995607a9-bad4-4151-b6d6-b92e9db6b774/dqc_reference
[2023-06-13 14:58:39,927] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:58:39,928] [INFO] Task started: Prodigal
[2023-06-13 14:58:39,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bc4309f-d636-42c2-8903-7907c7ce5ea2/GCA_947449235.1_Jr-14may18-326_genomic.fna.gz | prodigal -d GCA_947449235.1_Jr-14may18-326_genomic.fna/cds.fna -a GCA_947449235.1_Jr-14may18-326_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:58:43,018] [INFO] Task succeeded: Prodigal
[2023-06-13 14:58:43,018] [INFO] Task started: HMMsearch
[2023-06-13 14:58:43,018] [INFO] Running command: hmmsearch --tblout GCA_947449235.1_Jr-14may18-326_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg995607a9-bad4-4151-b6d6-b92e9db6b774/dqc_reference/reference_markers.hmm GCA_947449235.1_Jr-14may18-326_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:58:43,153] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:58:43,154] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5bc4309f-d636-42c2-8903-7907c7ce5ea2/GCA_947449235.1_Jr-14may18-326_genomic.fna.gz]
[2023-06-13 14:58:43,169] [INFO] Query marker FASTA was written to GCA_947449235.1_Jr-14may18-326_genomic.fna/markers.fasta
[2023-06-13 14:58:43,169] [INFO] Task started: Blastn
[2023-06-13 14:58:43,169] [INFO] Running command: blastn -query GCA_947449235.1_Jr-14may18-326_genomic.fna/markers.fasta -db /var/lib/cwl/stg995607a9-bad4-4151-b6d6-b92e9db6b774/dqc_reference/reference_markers.fasta -out GCA_947449235.1_Jr-14may18-326_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:58:43,643] [INFO] Task succeeded: Blastn
[2023-06-13 14:58:43,647] [INFO] Selected 13 target genomes.
[2023-06-13 14:58:43,647] [INFO] Target genome list was writen to GCA_947449235.1_Jr-14may18-326_genomic.fna/target_genomes.txt
[2023-06-13 14:58:43,651] [INFO] Task started: fastANI
[2023-06-13 14:58:43,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bc4309f-d636-42c2-8903-7907c7ce5ea2/GCA_947449235.1_Jr-14may18-326_genomic.fna.gz --refList GCA_947449235.1_Jr-14may18-326_genomic.fna/target_genomes.txt --output GCA_947449235.1_Jr-14may18-326_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:58:55,589] [INFO] Task succeeded: fastANI
[2023-06-13 14:58:55,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg995607a9-bad4-4151-b6d6-b92e9db6b774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:58:55,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg995607a9-bad4-4151-b6d6-b92e9db6b774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:58:55,591] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:58:55,592] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:58:55,592] [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
--------------------------------------------------------------------------------
[2023-06-13 14:58:55,596] [INFO] DFAST Taxonomy check result was written to GCA_947449235.1_Jr-14may18-326_genomic.fna/tc_result.tsv
[2023-06-13 14:58:55,596] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:58:55,596] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:58:55,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg995607a9-bad4-4151-b6d6-b92e9db6b774/dqc_reference/checkm_data
[2023-06-13 14:58:55,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:58:55,633] [INFO] Task started: CheckM
[2023-06-13 14:58:55,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947449235.1_Jr-14may18-326_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947449235.1_Jr-14may18-326_genomic.fna/checkm_input GCA_947449235.1_Jr-14may18-326_genomic.fna/checkm_result
[2023-06-13 14:59:12,164] [INFO] Task succeeded: CheckM
[2023-06-13 14:59:12,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 14:59:12,184] [INFO] ===== Completeness check finished =====
[2023-06-13 14:59:12,185] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:59:12,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947449235.1_Jr-14may18-326_genomic.fna/markers.fasta)
[2023-06-13 14:59:12,185] [INFO] Task started: Blastn
[2023-06-13 14:59:12,185] [INFO] Running command: blastn -query GCA_947449235.1_Jr-14may18-326_genomic.fna/markers.fasta -db /var/lib/cwl/stg995607a9-bad4-4151-b6d6-b92e9db6b774/dqc_reference/reference_markers_gtdb.fasta -out GCA_947449235.1_Jr-14may18-326_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:12,682] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:12,686] [INFO] Selected 19 target genomes.
[2023-06-13 14:59:12,686] [INFO] Target genome list was writen to GCA_947449235.1_Jr-14may18-326_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:59:12,691] [INFO] Task started: fastANI
[2023-06-13 14:59:12,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bc4309f-d636-42c2-8903-7907c7ce5ea2/GCA_947449235.1_Jr-14may18-326_genomic.fna.gz --refList GCA_947449235.1_Jr-14may18-326_genomic.fna/target_genomes_gtdb.txt --output GCA_947449235.1_Jr-14may18-326_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:59:19,384] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:19,389] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:59:19,389] [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_009701115.1	s__RAAP-2 sp009701115	88.4318	212	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726065.1	s__RAAP-2 sp009726065	84.5	213	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885505.1	s__RAAP-2 sp903885505	78.8962	51	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.39	99.28	0.89	0.87	3	-
GCA_903871335.1	s__RAAP-2 sp903871335	77.3229	61	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	98.60	0.98	0.96	25	-
--------------------------------------------------------------------------------
[2023-06-13 14:59:19,391] [INFO] GTDB search result was written to GCA_947449235.1_Jr-14may18-326_genomic.fna/result_gtdb.tsv
[2023-06-13 14:59:19,391] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:59:19,394] [INFO] DFAST_QC result json was written to GCA_947449235.1_Jr-14may18-326_genomic.fna/dqc_result.json
[2023-06-13 14:59:19,394] [INFO] DFAST_QC completed!
[2023-06-13 14:59:19,394] [INFO] Total running time: 0h0m41s