[2023-06-18 14:01:56,806] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:01:56,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:01:56,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d8fec16-4572-4a9b-b555-cf3148b517ac/dqc_reference
[2023-06-18 14:02:00,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:02:00,749] [INFO] Task started: Prodigal
[2023-06-18 14:02:00,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3906ed2-810f-4edf-990d-c20ee5d04680/GCA_018655355.1_ASM1865535v1_genomic.fna.gz | prodigal -d GCA_018655355.1_ASM1865535v1_genomic.fna/cds.fna -a GCA_018655355.1_ASM1865535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:02:08,826] [INFO] Task succeeded: Prodigal
[2023-06-18 14:02:08,827] [INFO] Task started: HMMsearch
[2023-06-18 14:02:08,827] [INFO] Running command: hmmsearch --tblout GCA_018655355.1_ASM1865535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d8fec16-4572-4a9b-b555-cf3148b517ac/dqc_reference/reference_markers.hmm GCA_018655355.1_ASM1865535v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:02:09,146] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:02:09,147] [INFO] Found 6/6 markers.
[2023-06-18 14:02:09,185] [INFO] Query marker FASTA was written to GCA_018655355.1_ASM1865535v1_genomic.fna/markers.fasta
[2023-06-18 14:02:09,185] [INFO] Task started: Blastn
[2023-06-18 14:02:09,185] [INFO] Running command: blastn -query GCA_018655355.1_ASM1865535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d8fec16-4572-4a9b-b555-cf3148b517ac/dqc_reference/reference_markers.fasta -out GCA_018655355.1_ASM1865535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:02:09,842] [INFO] Task succeeded: Blastn
[2023-06-18 14:02:09,845] [INFO] Selected 24 target genomes.
[2023-06-18 14:02:09,846] [INFO] Target genome list was writen to GCA_018655355.1_ASM1865535v1_genomic.fna/target_genomes.txt
[2023-06-18 14:02:09,871] [INFO] Task started: fastANI
[2023-06-18 14:02:09,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3906ed2-810f-4edf-990d-c20ee5d04680/GCA_018655355.1_ASM1865535v1_genomic.fna.gz --refList GCA_018655355.1_ASM1865535v1_genomic.fna/target_genomes.txt --output GCA_018655355.1_ASM1865535v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:02:24,406] [INFO] Task succeeded: fastANI
[2023-06-18 14:02:24,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d8fec16-4572-4a9b-b555-cf3148b517ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:02:24,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d8fec16-4572-4a9b-b555-cf3148b517ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:02:24,409] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:02:24,410] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 14:02:24,410] [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
--------------------------------------------------------------------------------
[2023-06-18 14:02:24,412] [INFO] DFAST Taxonomy check result was written to GCA_018655355.1_ASM1865535v1_genomic.fna/tc_result.tsv
[2023-06-18 14:02:24,413] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:02:24,413] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:02:24,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d8fec16-4572-4a9b-b555-cf3148b517ac/dqc_reference/checkm_data
[2023-06-18 14:02:24,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:02:24,456] [INFO] Task started: CheckM
[2023-06-18 14:02:24,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018655355.1_ASM1865535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018655355.1_ASM1865535v1_genomic.fna/checkm_input GCA_018655355.1_ASM1865535v1_genomic.fna/checkm_result
[2023-06-18 14:02:54,357] [INFO] Task succeeded: CheckM
[2023-06-18 14:02:54,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 14:02:54,381] [INFO] ===== Completeness check finished =====
[2023-06-18 14:02:54,381] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:02:54,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018655355.1_ASM1865535v1_genomic.fna/markers.fasta)
[2023-06-18 14:02:54,382] [INFO] Task started: Blastn
[2023-06-18 14:02:54,382] [INFO] Running command: blastn -query GCA_018655355.1_ASM1865535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d8fec16-4572-4a9b-b555-cf3148b517ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_018655355.1_ASM1865535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:02:55,384] [INFO] Task succeeded: Blastn
[2023-06-18 14:02:55,389] [INFO] Selected 10 target genomes.
[2023-06-18 14:02:55,389] [INFO] Target genome list was writen to GCA_018655355.1_ASM1865535v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:02:55,393] [INFO] Task started: fastANI
[2023-06-18 14:02:55,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3906ed2-810f-4edf-990d-c20ee5d04680/GCA_018655355.1_ASM1865535v1_genomic.fna.gz --refList GCA_018655355.1_ASM1865535v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018655355.1_ASM1865535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:03:00,838] [INFO] Task succeeded: fastANI
[2023-06-18 14:03:00,846] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 14:03:00,847] [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_018653085.1	s__LS-NOB sp018653085	99.8621	962	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	conclusive
GCA_003545625.1	s__LS-NOB sp003545625	86.7089	450	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_001542995.1	s__LS-NOB sp001542995	81.3295	630	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	80.4295	601	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_018673915.1	s__LS-NOB sp018673915	80.2126	631	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.92	99.88	0.94	0.90	12	-
GCA_002786505.1	s__LS-NOB sp002786505	79.8105	446	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664975.1	s__LS-NOB sp018664975	79.564	491	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454045.1	s__LS-NOB sp002454045	78.7974	378	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.99	99.99	0.99	0.99	2	-
GCA_012961055.1	s__LS-NOB sp012961055	78.6373	240	995	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 14:03:00,849] [INFO] GTDB search result was written to GCA_018655355.1_ASM1865535v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:03:00,849] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:03:00,853] [INFO] DFAST_QC result json was written to GCA_018655355.1_ASM1865535v1_genomic.fna/dqc_result.json
[2023-06-18 14:03:00,853] [INFO] DFAST_QC completed!
[2023-06-18 14:03:00,854] [INFO] Total running time: 0h1m4s