[2024-01-24 12:53:56,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg6df337cc-14ee-4577-9a40-1147be0470f2/dqc_reference
[2024-01-24 12:53:58,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,025] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg63f9fa0f-84e6-4ffc-a14a-a1b952b8b2d1/GCF_003863965.1_ASM386396v1_genomic.fna.gz | prodigal -d GCF_003863965.1_ASM386396v1_genomic.fna/cds.fna -a GCF_003863965.1_ASM386396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:20,667] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:20,667] [INFO] Task started: HMMsearch
[2024-01-24 12:54:20,667] [INFO] Running command: hmmsearch --tblout GCF_003863965.1_ASM386396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6df337cc-14ee-4577-9a40-1147be0470f2/dqc_reference/reference_markers.hmm GCF_003863965.1_ASM386396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:21,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:21,166] [INFO] Found 6/6 markers.
[2024-01-24 12:54:21,245] [INFO] Query marker FASTA was written to GCF_003863965.1_ASM386396v1_genomic.fna/markers.fasta
[2024-01-24 12:54:21,246] [INFO] Task started: Blastn
[2024-01-24 12:54:21,246] [INFO] Running command: blastn -query GCF_003863965.1_ASM386396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df337cc-14ee-4577-9a40-1147be0470f2/dqc_reference/reference_markers.fasta -out GCF_003863965.1_ASM386396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:21,917] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:21,921] [INFO] Selected 9 target genomes.
[2024-01-24 12:54:21,922] [INFO] Target genome list was writen to GCF_003863965.1_ASM386396v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:21,931] [INFO] Task started: fastANI
[2024-01-24 12:54:21,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg63f9fa0f-84e6-4ffc-a14a-a1b952b8b2d1/GCF_003863965.1_ASM386396v1_genomic.fna.gz --refList GCF_003863965.1_ASM386396v1_genomic.fna/target_genomes.txt --output GCF_003863965.1_ASM386396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:39,709] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:39,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6df337cc-14ee-4577-9a40-1147be0470f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:39,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6df337cc-14ee-4577-9a40-1147be0470f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:39,721] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:39,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:39,721] [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
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	100.0	2697	2700	95	conclusive
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	91.7052	1830	2700	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	91.6977	1952	2700	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	91.6309	1956	2700	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	80.4841	846	2700	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	80.3402	817	2700	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.9184	267	2700	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.785	150	2700	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.6463	240	2700	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:39,723] [INFO] DFAST Taxonomy check result was written to GCF_003863965.1_ASM386396v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:39,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:39,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:39,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6df337cc-14ee-4577-9a40-1147be0470f2/dqc_reference/checkm_data
[2024-01-24 12:54:39,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:39,800] [INFO] Task started: CheckM
[2024-01-24 12:54:39,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003863965.1_ASM386396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003863965.1_ASM386396v1_genomic.fna/checkm_input GCF_003863965.1_ASM386396v1_genomic.fna/checkm_result
[2024-01-24 12:55:40,226] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:40,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:40,251] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:40,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:40,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003863965.1_ASM386396v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:40,252] [INFO] Task started: Blastn
[2024-01-24 12:55:40,252] [INFO] Running command: blastn -query GCF_003863965.1_ASM386396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df337cc-14ee-4577-9a40-1147be0470f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003863965.1_ASM386396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:41,037] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:41,041] [INFO] Selected 7 target genomes.
[2024-01-24 12:55:41,041] [INFO] Target genome list was writen to GCF_003863965.1_ASM386396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:41,046] [INFO] Task started: fastANI
[2024-01-24 12:55:41,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg63f9fa0f-84e6-4ffc-a14a-a1b952b8b2d1/GCF_003863965.1_ASM386396v1_genomic.fna.gz --refList GCF_003863965.1_ASM386396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003863965.1_ASM386396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:55,761] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:55,769] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:55,769] [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_003863965.1	s__Paenibacillus_A oralis	100.0	2697	2700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900454495.1	s__Paenibacillus_A macerans	91.6807	1955	2700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	80.4834	906	2700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900021165.1	s__Paenibacillus_A phocaensis	80.4702	846	2700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	79.7922	781	2700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000159955.1	s__Paenibacillus_A sp000159955	79.7692	698	2700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725205.1	s__Paenibacillus_A timonensis	79.7271	730	2700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:55,775] [INFO] GTDB search result was written to GCF_003863965.1_ASM386396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:55,776] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:55,779] [INFO] DFAST_QC result json was written to GCF_003863965.1_ASM386396v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:55,779] [INFO] DFAST_QC completed!
[2024-01-24 12:55:55,779] [INFO] Total running time: 0h1m59s