[2024-01-24 13:02:03,893] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,895] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dce825e-9bec-4abd-82c0-89a92c2e620f/dqc_reference
[2024-01-24 13:02:05,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,340] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a15ea4d-e087-414a-83df-7df82c015a4b/GCF_000688455.1_ASM68845v1_genomic.fna.gz | prodigal -d GCF_000688455.1_ASM68845v1_genomic.fna/cds.fna -a GCF_000688455.1_ASM68845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:17,462] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:17,463] [INFO] Task started: HMMsearch
[2024-01-24 13:02:17,463] [INFO] Running command: hmmsearch --tblout GCF_000688455.1_ASM68845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dce825e-9bec-4abd-82c0-89a92c2e620f/dqc_reference/reference_markers.hmm GCF_000688455.1_ASM68845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:17,770] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:17,771] [INFO] Found 6/6 markers.
[2024-01-24 13:02:17,806] [INFO] Query marker FASTA was written to GCF_000688455.1_ASM68845v1_genomic.fna/markers.fasta
[2024-01-24 13:02:17,806] [INFO] Task started: Blastn
[2024-01-24 13:02:17,806] [INFO] Running command: blastn -query GCF_000688455.1_ASM68845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dce825e-9bec-4abd-82c0-89a92c2e620f/dqc_reference/reference_markers.fasta -out GCF_000688455.1_ASM68845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:18,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:18,428] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:18,429] [INFO] Target genome list was writen to GCF_000688455.1_ASM68845v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:18,436] [INFO] Task started: fastANI
[2024-01-24 13:02:18,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a15ea4d-e087-414a-83df-7df82c015a4b/GCF_000688455.1_ASM68845v1_genomic.fna.gz --refList GCF_000688455.1_ASM68845v1_genomic.fna/target_genomes.txt --output GCF_000688455.1_ASM68845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:28,464] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:28,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dce825e-9bec-4abd-82c0-89a92c2e620f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:28,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dce825e-9bec-4abd-82c0-89a92c2e620f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:28,477] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:28,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:28,478] [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
Pseudacidobacterium ailaaui	strain=PMMR2	GCA_000688455.1	1382359	1382359	type	True	100.0	1228	1228	95	conclusive
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	77.2282	195	1228	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.0907	148	1228	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.9549	154	1228	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.7139	143	1228	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.6848	143	1228	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.6262	133	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:28,480] [INFO] DFAST Taxonomy check result was written to GCF_000688455.1_ASM68845v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:28,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:28,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:28,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dce825e-9bec-4abd-82c0-89a92c2e620f/dqc_reference/checkm_data
[2024-01-24 13:02:28,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:28,519] [INFO] Task started: CheckM
[2024-01-24 13:02:28,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000688455.1_ASM68845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000688455.1_ASM68845v1_genomic.fna/checkm_input GCF_000688455.1_ASM68845v1_genomic.fna/checkm_result
[2024-01-24 13:03:06,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:06,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:06,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:06,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:06,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000688455.1_ASM68845v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:06,254] [INFO] Task started: Blastn
[2024-01-24 13:03:06,255] [INFO] Running command: blastn -query GCF_000688455.1_ASM68845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dce825e-9bec-4abd-82c0-89a92c2e620f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000688455.1_ASM68845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:07,104] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:07,108] [INFO] Selected 12 target genomes.
[2024-01-24 13:03:07,108] [INFO] Target genome list was writen to GCF_000688455.1_ASM68845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:07,119] [INFO] Task started: fastANI
[2024-01-24 13:03:07,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a15ea4d-e087-414a-83df-7df82c015a4b/GCF_000688455.1_ASM68845v1_genomic.fna.gz --refList GCF_000688455.1_ASM68845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000688455.1_ASM68845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:15,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:15,686] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:15,686] [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
GCF_000688455.1	s__Acidobacterium_A ailaaui	100.0	1228	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013285705.1	s__Acidobacterium_A sp013285705	77.3156	112	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274465.1	s__Acidobacterium_A sp014274465	77.2282	195	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	77.0907	148	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009765985.1	s__Acidobacterium_A sp009765985	77.0171	223	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	76.9713	133	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428625.2	s__Palsa-343 sp003428625	76.9549	154	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123295.1	s__Silvibacterium dinghuense	76.6848	143	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019234945.1	s__Silvibacterium sp019234945	76.6617	82	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339725.1	s__Acidipila rosea	76.6262	133	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidipila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655315.1	s__Acidobacterium_A sp015655315	76.5177	124	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858395.1	s__EB88 sp003858395	76.3569	80	1228	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__EB88	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:15,688] [INFO] GTDB search result was written to GCF_000688455.1_ASM68845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:15,688] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:15,692] [INFO] DFAST_QC result json was written to GCF_000688455.1_ASM68845v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:15,692] [INFO] DFAST_QC completed!
[2024-01-24 13:03:15,692] [INFO] Total running time: 0h1m12s