[2023-06-27 18:55:33,475] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:55:33,479] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:55:33,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg81893689-04ae-40a0-9d10-e5aa140b0dd5/dqc_reference
[2023-06-27 18:55:34,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:55:34,636] [INFO] Task started: Prodigal
[2023-06-27 18:55:34,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e4ee568-2e18-49fd-bf42-3f86c8f531e1/GCA_026708105.1_ASM2670810v1_genomic.fna.gz | prodigal -d GCA_026708105.1_ASM2670810v1_genomic.fna/cds.fna -a GCA_026708105.1_ASM2670810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:55:48,095] [INFO] Task succeeded: Prodigal
[2023-06-27 18:55:48,095] [INFO] Task started: HMMsearch
[2023-06-27 18:55:48,095] [INFO] Running command: hmmsearch --tblout GCA_026708105.1_ASM2670810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81893689-04ae-40a0-9d10-e5aa140b0dd5/dqc_reference/reference_markers.hmm GCA_026708105.1_ASM2670810v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:55:48,333] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:55:48,335] [INFO] Found 6/6 markers.
[2023-06-27 18:55:48,372] [INFO] Query marker FASTA was written to GCA_026708105.1_ASM2670810v1_genomic.fna/markers.fasta
[2023-06-27 18:55:48,372] [INFO] Task started: Blastn
[2023-06-27 18:55:48,372] [INFO] Running command: blastn -query GCA_026708105.1_ASM2670810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81893689-04ae-40a0-9d10-e5aa140b0dd5/dqc_reference/reference_markers.fasta -out GCA_026708105.1_ASM2670810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:55:48,964] [INFO] Task succeeded: Blastn
[2023-06-27 18:55:48,968] [INFO] Selected 29 target genomes.
[2023-06-27 18:55:48,968] [INFO] Target genome list was writen to GCA_026708105.1_ASM2670810v1_genomic.fna/target_genomes.txt
[2023-06-27 18:55:48,973] [INFO] Task started: fastANI
[2023-06-27 18:55:48,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4ee568-2e18-49fd-bf42-3f86c8f531e1/GCA_026708105.1_ASM2670810v1_genomic.fna.gz --refList GCA_026708105.1_ASM2670810v1_genomic.fna/target_genomes.txt --output GCA_026708105.1_ASM2670810v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:56:09,846] [INFO] Task succeeded: fastANI
[2023-06-27 18:56:09,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81893689-04ae-40a0-9d10-e5aa140b0dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:56:09,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81893689-04ae-40a0-9d10-e5aa140b0dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:56:09,854] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:56:09,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:56:09,855] [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	75.4572	80	1608	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	74.819	60	1608	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.7427	65	1608	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	74.7303	71	1608	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	74.7256	60	1608	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	74.6121	50	1608	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:56:09,857] [INFO] DFAST Taxonomy check result was written to GCA_026708105.1_ASM2670810v1_genomic.fna/tc_result.tsv
[2023-06-27 18:56:09,857] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:56:09,858] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:56:09,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81893689-04ae-40a0-9d10-e5aa140b0dd5/dqc_reference/checkm_data
[2023-06-27 18:56:09,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:56:09,905] [INFO] Task started: CheckM
[2023-06-27 18:56:09,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708105.1_ASM2670810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708105.1_ASM2670810v1_genomic.fna/checkm_input GCA_026708105.1_ASM2670810v1_genomic.fna/checkm_result
[2023-06-27 18:56:50,002] [INFO] Task succeeded: CheckM
[2023-06-27 18:56:50,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:56:50,022] [INFO] ===== Completeness check finished =====
[2023-06-27 18:56:50,022] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:56:50,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708105.1_ASM2670810v1_genomic.fna/markers.fasta)
[2023-06-27 18:56:50,023] [INFO] Task started: Blastn
[2023-06-27 18:56:50,023] [INFO] Running command: blastn -query GCA_026708105.1_ASM2670810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81893689-04ae-40a0-9d10-e5aa140b0dd5/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708105.1_ASM2670810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:50,853] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:50,857] [INFO] Selected 27 target genomes.
[2023-06-27 18:56:50,857] [INFO] Target genome list was writen to GCA_026708105.1_ASM2670810v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:56:50,867] [INFO] Task started: fastANI
[2023-06-27 18:56:50,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4ee568-2e18-49fd-bf42-3f86c8f531e1/GCA_026708105.1_ASM2670810v1_genomic.fna.gz --refList GCA_026708105.1_ASM2670810v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708105.1_ASM2670810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:57:12,358] [INFO] Task succeeded: fastANI
[2023-06-27 18:57:12,367] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:57:12,367] [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	79.3541	606	1608	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	79.2467	599	1608	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	79.1238	675	1608	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	78.8528	602	1608	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	78.6485	647	1608	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494005.1	s__S144-5 sp015494005	76.3725	114	1608	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003451595.1	s__Caldilinea sp003451595	76.0706	70	1608	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.85	99.85	0.94	0.94	2	-
GCA_018003515.1	s__JAGNDO01 sp018003515	75.9252	73	1608	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JAGNDO01	95.0	99.87	99.85	0.92	0.92	4	-
GCF_000281175.1	s__Caldilinea aerophila	75.4572	80	1608	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	97.04	95.81	0.94	0.92	4	-
GCA_016124945.1	s__RI-153 sp016124945	75.3824	123	1608	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__RI-153	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:57:12,369] [INFO] GTDB search result was written to GCA_026708105.1_ASM2670810v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:57:12,370] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:57:12,373] [INFO] DFAST_QC result json was written to GCA_026708105.1_ASM2670810v1_genomic.fna/dqc_result.json
[2023-06-27 18:57:12,373] [INFO] DFAST_QC completed!
[2023-06-27 18:57:12,373] [INFO] Total running time: 0h1m39s