[2024-01-25 18:25:05,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:05,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:05,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f12bce7-7111-438a-9478-cee43e5a3690/dqc_reference
[2024-01-25 18:25:06,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:06,841] [INFO] Task started: Prodigal
[2024-01-25 18:25:06,841] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e5ea35-53f1-4cce-ad64-98b38239de9b/GCF_002951875.1_ASM295187v1_genomic.fna.gz | prodigal -d GCF_002951875.1_ASM295187v1_genomic.fna/cds.fna -a GCF_002951875.1_ASM295187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:16,352] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:16,353] [INFO] Task started: HMMsearch
[2024-01-25 18:25:16,353] [INFO] Running command: hmmsearch --tblout GCF_002951875.1_ASM295187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f12bce7-7111-438a-9478-cee43e5a3690/dqc_reference/reference_markers.hmm GCF_002951875.1_ASM295187v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:16,605] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:16,606] [INFO] Found 6/6 markers.
[2024-01-25 18:25:16,638] [INFO] Query marker FASTA was written to GCF_002951875.1_ASM295187v1_genomic.fna/markers.fasta
[2024-01-25 18:25:16,639] [INFO] Task started: Blastn
[2024-01-25 18:25:16,639] [INFO] Running command: blastn -query GCF_002951875.1_ASM295187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f12bce7-7111-438a-9478-cee43e5a3690/dqc_reference/reference_markers.fasta -out GCF_002951875.1_ASM295187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:17,176] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:17,179] [INFO] Selected 21 target genomes.
[2024-01-25 18:25:17,179] [INFO] Target genome list was writen to GCF_002951875.1_ASM295187v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:17,197] [INFO] Task started: fastANI
[2024-01-25 18:25:17,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e5ea35-53f1-4cce-ad64-98b38239de9b/GCF_002951875.1_ASM295187v1_genomic.fna.gz --refList GCF_002951875.1_ASM295187v1_genomic.fna/target_genomes.txt --output GCF_002951875.1_ASM295187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:37,632] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:37,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f12bce7-7111-438a-9478-cee43e5a3690/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:37,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f12bce7-7111-438a-9478-cee43e5a3690/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:37,638] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:25:37,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:25:37,638] [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 larvae subsp. larvae	strain=ERIC_I	GCA_002951875.1	147375	1464	type	True	100.0	1425	1429	95	conclusive
Paenibacillus larvae subsp. larvae	strain=ATCC 9545	GCA_002003265.1	147375	1464	type	True	99.9716	1417	1429	95	conclusive
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	77.6143	63	1429	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	76.9699	64	1429	95	below_threshold
Paenibacillus eucommiae	strain=DSM 26048	GCA_017874215.1	1355755	1355755	type	True	76.8999	70	1429	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	76.883	71	1429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:37,640] [INFO] DFAST Taxonomy check result was written to GCF_002951875.1_ASM295187v1_genomic.fna/tc_result.tsv
[2024-01-25 18:25:37,640] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:37,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:37,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f12bce7-7111-438a-9478-cee43e5a3690/dqc_reference/checkm_data
[2024-01-25 18:25:37,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:37,684] [INFO] Task started: CheckM
[2024-01-25 18:25:37,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002951875.1_ASM295187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002951875.1_ASM295187v1_genomic.fna/checkm_input GCF_002951875.1_ASM295187v1_genomic.fna/checkm_result
[2024-01-25 18:26:09,085] [INFO] Task succeeded: CheckM
[2024-01-25 18:26:09,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:26:09,108] [INFO] ===== Completeness check finished =====
[2024-01-25 18:26:09,108] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:26:09,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002951875.1_ASM295187v1_genomic.fna/markers.fasta)
[2024-01-25 18:26:09,109] [INFO] Task started: Blastn
[2024-01-25 18:26:09,109] [INFO] Running command: blastn -query GCF_002951875.1_ASM295187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f12bce7-7111-438a-9478-cee43e5a3690/dqc_reference/reference_markers_gtdb.fasta -out GCF_002951875.1_ASM295187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:26:09,903] [INFO] Task succeeded: Blastn
[2024-01-25 18:26:09,907] [INFO] Selected 26 target genomes.
[2024-01-25 18:26:09,907] [INFO] Target genome list was writen to GCF_002951875.1_ASM295187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:26:09,929] [INFO] Task started: fastANI
[2024-01-25 18:26:09,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e5ea35-53f1-4cce-ad64-98b38239de9b/GCF_002951875.1_ASM295187v1_genomic.fna.gz --refList GCF_002951875.1_ASM295187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002951875.1_ASM295187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:26:37,905] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:37,912] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:26:37,913] [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_002003265.1	s__Paenibacillus_H larvae	99.9716	1416	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_H	95.0	99.26	98.58	0.93	0.88	15	conclusive
GCF_013401555.1	s__Paenibacillus sp900110055	79.2489	54	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.27	96.55	0.92	0.89	5	-
GCF_900177425.1	s__Paenibacillus uliginis	77.586	64	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204845.1	s__Paenibacillus_E qinlingensis	77.4783	56	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428105.1	s__Paenibacillus_E sp001428105	77.2167	52	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234615.1	s__Paenibacillus_S rigui	77.0102	63	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003955665.1	s__Paenibacillus_E whitsoniae	76.962	62	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874215.1	s__Paenibacillus_AI eucommiae	76.9054	71	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679495.1	s__Paenibacillus_L sp007679495	76.7882	52	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_L	95.0	99.12	99.12	0.91	0.91	2	-
GCF_000686845.1	s__Paenibacillus_S sp000686845	76.5971	69	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:26:37,914] [INFO] GTDB search result was written to GCF_002951875.1_ASM295187v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:26:37,915] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:26:37,917] [INFO] DFAST_QC result json was written to GCF_002951875.1_ASM295187v1_genomic.fna/dqc_result.json
[2024-01-25 18:26:37,917] [INFO] DFAST_QC completed!
[2024-01-25 18:26:37,917] [INFO] Total running time: 0h1m32s