[2023-06-27 17:41:08,084] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:08,087] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:08,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg76c1663d-ae24-42f6-8d4f-f089d044ba53/dqc_reference
[2023-06-27 17:41:09,723] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:09,724] [INFO] Task started: Prodigal
[2023-06-27 17:41:09,724] [INFO] Running command: gunzip -c /var/lib/cwl/stgff6c1449-8162-4666-ba97-bd8c32ad7709/GCA_026708085.1_ASM2670808v1_genomic.fna.gz | prodigal -d GCA_026708085.1_ASM2670808v1_genomic.fna/cds.fna -a GCA_026708085.1_ASM2670808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:26,798] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:26,798] [INFO] Task started: HMMsearch
[2023-06-27 17:41:26,798] [INFO] Running command: hmmsearch --tblout GCA_026708085.1_ASM2670808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76c1663d-ae24-42f6-8d4f-f089d044ba53/dqc_reference/reference_markers.hmm GCA_026708085.1_ASM2670808v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:27,129] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:27,131] [INFO] Found 6/6 markers.
[2023-06-27 17:41:27,188] [INFO] Query marker FASTA was written to GCA_026708085.1_ASM2670808v1_genomic.fna/markers.fasta
[2023-06-27 17:41:27,188] [INFO] Task started: Blastn
[2023-06-27 17:41:27,188] [INFO] Running command: blastn -query GCA_026708085.1_ASM2670808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76c1663d-ae24-42f6-8d4f-f089d044ba53/dqc_reference/reference_markers.fasta -out GCA_026708085.1_ASM2670808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:27,822] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:27,826] [INFO] Selected 23 target genomes.
[2023-06-27 17:41:27,827] [INFO] Target genome list was writen to GCA_026708085.1_ASM2670808v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:27,834] [INFO] Task started: fastANI
[2023-06-27 17:41:27,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgff6c1449-8162-4666-ba97-bd8c32ad7709/GCA_026708085.1_ASM2670808v1_genomic.fna.gz --refList GCA_026708085.1_ASM2670808v1_genomic.fna/target_genomes.txt --output GCA_026708085.1_ASM2670808v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:41:45,486] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:45,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76c1663d-ae24-42f6-8d4f-f089d044ba53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:41:45,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76c1663d-ae24-42f6-8d4f-f089d044ba53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:41:45,490] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:41:45,490] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 17:41:45,490] [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
Caldilinea aerophila	strain=DSM 14535	GCA_000281175.1	133453	133453	type	True	75.4587	72	1979	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 17:41:45,492] [INFO] DFAST Taxonomy check result was written to GCA_026708085.1_ASM2670808v1_genomic.fna/tc_result.tsv
[2023-06-27 17:41:45,493] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:41:45,493] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:45,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76c1663d-ae24-42f6-8d4f-f089d044ba53/dqc_reference/checkm_data
[2023-06-27 17:41:45,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:45,555] [INFO] Task started: CheckM
[2023-06-27 17:41:45,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708085.1_ASM2670808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708085.1_ASM2670808v1_genomic.fna/checkm_input GCA_026708085.1_ASM2670808v1_genomic.fna/checkm_result
[2023-06-27 17:42:34,282] [INFO] Task succeeded: CheckM
[2023-06-27 17:42:34,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:42:34,324] [INFO] ===== Completeness check finished =====
[2023-06-27 17:42:34,325] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:42:34,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708085.1_ASM2670808v1_genomic.fna/markers.fasta)
[2023-06-27 17:42:34,325] [INFO] Task started: Blastn
[2023-06-27 17:42:34,326] [INFO] Running command: blastn -query GCA_026708085.1_ASM2670808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76c1663d-ae24-42f6-8d4f-f089d044ba53/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708085.1_ASM2670808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:42:35,166] [INFO] Task succeeded: Blastn
[2023-06-27 17:42:35,172] [INFO] Selected 10 target genomes.
[2023-06-27 17:42:35,172] [INFO] Target genome list was writen to GCA_026708085.1_ASM2670808v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:42:35,176] [INFO] Task started: fastANI
[2023-06-27 17:42:35,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgff6c1449-8162-4666-ba97-bd8c32ad7709/GCA_026708085.1_ASM2670808v1_genomic.fna.gz --refList GCA_026708085.1_ASM2670808v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708085.1_ASM2670808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:42:45,470] [INFO] Task succeeded: fastANI
[2023-06-27 17:42:45,481] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 17:42:45,481] [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_011523365.1	s__Bin5 sp011523365	89.0746	1474	1979	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840225.1	s__Bin5 sp009840225	88.8996	1364	1979	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	97.63	95.35	0.89	0.84	3	-
GCA_009841235.1	s__Bin5 sp009841235	85.2839	1359	1979	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	95.53	95.53	0.91	0.91	2	-
GCA_009838625.1	s__Bin5 sp009838625	84.682	1275	1979	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	99.90	99.90	0.97	0.97	2	-
GCA_002238445.1	s__Bin5 sp002238445	82.0158	1080	1979	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199425.1	s__JACQGT01 sp016199425	75.702	61	1979	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JACQGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281175.1	s__Caldilinea aerophila	75.4735	71	1979	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	97.04	95.81	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-27 17:42:45,483] [INFO] GTDB search result was written to GCA_026708085.1_ASM2670808v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:42:45,484] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:42:45,490] [INFO] DFAST_QC result json was written to GCA_026708085.1_ASM2670808v1_genomic.fna/dqc_result.json
[2023-06-27 17:42:45,490] [INFO] DFAST_QC completed!
[2023-06-27 17:42:45,490] [INFO] Total running time: 0h1m37s