[2024-01-24 12:27:19,645] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:19,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:19,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a32323d-f859-421d-83df-d3424bcb055b/dqc_reference
[2024-01-24 12:27:20,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,841] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgf426be02-7b82-43b1-9e5c-253f250862f7/GCF_009757995.1_ASM975799v1_genomic.fna.gz | prodigal -d GCF_009757995.1_ASM975799v1_genomic.fna/cds.fna -a GCF_009757995.1_ASM975799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:43,085] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:43,086] [INFO] Task started: HMMsearch
[2024-01-24 12:27:43,086] [INFO] Running command: hmmsearch --tblout GCF_009757995.1_ASM975799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a32323d-f859-421d-83df-d3424bcb055b/dqc_reference/reference_markers.hmm GCF_009757995.1_ASM975799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:43,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:43,471] [INFO] Found 6/6 markers.
[2024-01-24 12:27:43,542] [INFO] Query marker FASTA was written to GCF_009757995.1_ASM975799v1_genomic.fna/markers.fasta
[2024-01-24 12:27:43,542] [INFO] Task started: Blastn
[2024-01-24 12:27:43,542] [INFO] Running command: blastn -query GCF_009757995.1_ASM975799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a32323d-f859-421d-83df-d3424bcb055b/dqc_reference/reference_markers.fasta -out GCF_009757995.1_ASM975799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:44,132] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:44,136] [INFO] Selected 10 target genomes.
[2024-01-24 12:27:44,137] [INFO] Target genome list was writen to GCF_009757995.1_ASM975799v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:44,151] [INFO] Task started: fastANI
[2024-01-24 12:27:44,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgf426be02-7b82-43b1-9e5c-253f250862f7/GCF_009757995.1_ASM975799v1_genomic.fna.gz --refList GCF_009757995.1_ASM975799v1_genomic.fna/target_genomes.txt --output GCF_009757995.1_ASM975799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:58,668] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:58,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a32323d-f859-421d-83df-d3424bcb055b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:58,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a32323d-f859-421d-83df-d3424bcb055b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:58,680] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:27:58,680] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:27:58,681] [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 anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	100.0	2858	2862	95	inconclusive
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	95.9633	2322	2862	95	inconclusive
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	88.0159	2139	2862	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	84.7025	1694	2862	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	84.1879	1521	2862	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	77.4385	186	2862	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.2191	59	2862	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.847	129	2862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:27:58,682] [INFO] DFAST Taxonomy check result was written to GCF_009757995.1_ASM975799v1_genomic.fna/tc_result.tsv
[2024-01-24 12:27:58,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:58,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:58,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a32323d-f859-421d-83df-d3424bcb055b/dqc_reference/checkm_data
[2024-01-24 12:27:58,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:58,761] [INFO] Task started: CheckM
[2024-01-24 12:27:58,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009757995.1_ASM975799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009757995.1_ASM975799v1_genomic.fna/checkm_input GCF_009757995.1_ASM975799v1_genomic.fna/checkm_result
[2024-01-24 12:29:03,735] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:03,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:03,764] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:03,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:03,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009757995.1_ASM975799v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:03,766] [INFO] Task started: Blastn
[2024-01-24 12:29:03,766] [INFO] Running command: blastn -query GCF_009757995.1_ASM975799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a32323d-f859-421d-83df-d3424bcb055b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009757995.1_ASM975799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:04,482] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:04,487] [INFO] Selected 5 target genomes.
[2024-01-24 12:29:04,487] [INFO] Target genome list was writen to GCF_009757995.1_ASM975799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:04,520] [INFO] Task started: fastANI
[2024-01-24 12:29:04,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgf426be02-7b82-43b1-9e5c-253f250862f7/GCF_009757995.1_ASM975799v1_genomic.fna.gz --refList GCF_009757995.1_ASM975799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009757995.1_ASM975799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:14,492] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:14,502] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:14,502] [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_004000765.1	s__Paenibacillus_E chondroitinus	95.958	2322	2862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	96.01	96.01	0.90	0.90	3	conclusive
GCF_009882985.1	s__Paenibacillus_E silvestris	88.0189	2139	2862	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_007829615.1	s__Paenibacillus_E sp007829615	87.6354	2187	2862	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_017874035.1	s__Paenibacillus_E aceris	84.6808	1698	2862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013141725.1	s__Paenibacillus_E planticolens	84.1974	1520	2862	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:14,504] [INFO] GTDB search result was written to GCF_009757995.1_ASM975799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:14,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:14,508] [INFO] DFAST_QC result json was written to GCF_009757995.1_ASM975799v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:14,508] [INFO] DFAST_QC completed!
[2024-01-24 12:29:14,509] [INFO] Total running time: 0h1m55s