[2024-01-24 13:36:30,841] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:30,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:30,844] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd36b60a-c1a2-4a83-8ecc-330203652bba/dqc_reference
[2024-01-24 13:36:32,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,204] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,205] [INFO] Running command: gunzip -c /var/lib/cwl/stgf715d4f8-4783-4125-9341-61f9c91a5a03/GCF_007845635.1_ASM784563v1_genomic.fna.gz | prodigal -d GCF_007845635.1_ASM784563v1_genomic.fna/cds.fna -a GCF_007845635.1_ASM784563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:39,278] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:39,278] [INFO] Task started: HMMsearch
[2024-01-24 13:36:39,278] [INFO] Running command: hmmsearch --tblout GCF_007845635.1_ASM784563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd36b60a-c1a2-4a83-8ecc-330203652bba/dqc_reference/reference_markers.hmm GCF_007845635.1_ASM784563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:39,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:39,511] [INFO] Found 6/6 markers.
[2024-01-24 13:36:39,536] [INFO] Query marker FASTA was written to GCF_007845635.1_ASM784563v1_genomic.fna/markers.fasta
[2024-01-24 13:36:39,536] [INFO] Task started: Blastn
[2024-01-24 13:36:39,536] [INFO] Running command: blastn -query GCF_007845635.1_ASM784563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd36b60a-c1a2-4a83-8ecc-330203652bba/dqc_reference/reference_markers.fasta -out GCF_007845635.1_ASM784563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:40,184] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:40,189] [INFO] Selected 27 target genomes.
[2024-01-24 13:36:40,190] [INFO] Target genome list was writen to GCF_007845635.1_ASM784563v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:40,225] [INFO] Task started: fastANI
[2024-01-24 13:36:40,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgf715d4f8-4783-4125-9341-61f9c91a5a03/GCF_007845635.1_ASM784563v1_genomic.fna.gz --refList GCF_007845635.1_ASM784563v1_genomic.fna/target_genomes.txt --output GCF_007845635.1_ASM784563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:53,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:53,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd36b60a-c1a2-4a83-8ecc-330203652bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:53,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd36b60a-c1a2-4a83-8ecc-330203652bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:53,900] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:53,900] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:53,901] [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
Apibacter muscae	strain=G8	GCA_007845635.1	2509004	2509004	type	True	100.0	814	815	95	conclusive
Apibacter adventoris	strain=wkB301	GCA_002964975.1	1679466	1679466	type	True	77.1419	193	815	95	below_threshold
Apibacter mensalis	strain=R-53146	GCA_001418685.1	1586267	1586267	type	True	77.1096	148	815	95	below_threshold
Apibacter mensalis	strain=R-53146	GCA_900018365.1	1586267	1586267	type	True	77.0928	149	815	95	below_threshold
Apibacter raozihei	strain=HY041	GCA_004014855.1	2500547	2500547	type	True	76.9006	169	815	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.0954	57	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:53,903] [INFO] DFAST Taxonomy check result was written to GCF_007845635.1_ASM784563v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:53,903] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:53,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:53,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd36b60a-c1a2-4a83-8ecc-330203652bba/dqc_reference/checkm_data
[2024-01-24 13:36:53,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:53,933] [INFO] Task started: CheckM
[2024-01-24 13:36:53,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007845635.1_ASM784563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007845635.1_ASM784563v1_genomic.fna/checkm_input GCF_007845635.1_ASM784563v1_genomic.fna/checkm_result
[2024-01-24 13:37:21,048] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:21,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:21,068] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:21,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:21,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007845635.1_ASM784563v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:21,070] [INFO] Task started: Blastn
[2024-01-24 13:37:21,070] [INFO] Running command: blastn -query GCF_007845635.1_ASM784563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd36b60a-c1a2-4a83-8ecc-330203652bba/dqc_reference/reference_markers_gtdb.fasta -out GCF_007845635.1_ASM784563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:22,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:22,105] [INFO] Selected 27 target genomes.
[2024-01-24 13:37:22,105] [INFO] Target genome list was writen to GCF_007845635.1_ASM784563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:22,178] [INFO] Task started: fastANI
[2024-01-24 13:37:22,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgf715d4f8-4783-4125-9341-61f9c91a5a03/GCF_007845635.1_ASM784563v1_genomic.fna.gz --refList GCF_007845635.1_ASM784563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007845635.1_ASM784563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:35,071] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,080] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:35,081] [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_007845635.1	s__Apibacter muscae	100.0	814	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	97.91	97.54	0.94	0.93	3	conclusive
GCF_011082725.1	s__Apibacter sp002964915	77.286	133	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	97.29	96.74	0.93	0.90	15	-
GCF_002964975.1	s__Apibacter adventoris	77.1545	193	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	98.15	98.15	0.92	0.92	2	-
GCF_001418685.1	s__Apibacter mensalis	77.0926	149	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004014855.1	s__Apibacter raozihei	76.8863	170	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	98.39	98.39	0.93	0.93	2	-
GCF_003260195.1	s__Lutibacter citreus	75.1029	56	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,082] [INFO] GTDB search result was written to GCF_007845635.1_ASM784563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:35,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:35,086] [INFO] DFAST_QC result json was written to GCF_007845635.1_ASM784563v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:35,087] [INFO] DFAST_QC completed!
[2024-01-24 13:37:35,087] [INFO] Total running time: 0h1m4s