[2024-01-24 10:56:34,829] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,831] [INFO] DQC Reference Directory: /var/lib/cwl/stgdccc90b3-0fae-4eb2-b008-d3a5494c411d/dqc_reference
[2024-01-24 10:56:36,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,716] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,716] [INFO] Running command: gunzip -c /var/lib/cwl/stge2c28020-7f3d-4141-978d-8e0031dbf1c4/GCF_025369935.1_ASM2536993v1_genomic.fna.gz | prodigal -d GCF_025369935.1_ASM2536993v1_genomic.fna/cds.fna -a GCF_025369935.1_ASM2536993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:56:56,064] [INFO] Task succeeded: Prodigal
[2024-01-24 10:56:56,064] [INFO] Task started: HMMsearch
[2024-01-24 10:56:56,065] [INFO] Running command: hmmsearch --tblout GCF_025369935.1_ASM2536993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdccc90b3-0fae-4eb2-b008-d3a5494c411d/dqc_reference/reference_markers.hmm GCF_025369935.1_ASM2536993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:56:56,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:56:56,411] [INFO] Found 6/6 markers.
[2024-01-24 10:56:56,470] [INFO] Query marker FASTA was written to GCF_025369935.1_ASM2536993v1_genomic.fna/markers.fasta
[2024-01-24 10:56:56,470] [INFO] Task started: Blastn
[2024-01-24 10:56:56,470] [INFO] Running command: blastn -query GCF_025369935.1_ASM2536993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdccc90b3-0fae-4eb2-b008-d3a5494c411d/dqc_reference/reference_markers.fasta -out GCF_025369935.1_ASM2536993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:56:57,059] [INFO] Task succeeded: Blastn
[2024-01-24 10:56:57,064] [INFO] Selected 9 target genomes.
[2024-01-24 10:56:57,064] [INFO] Target genome list was writen to GCF_025369935.1_ASM2536993v1_genomic.fna/target_genomes.txt
[2024-01-24 10:56:57,070] [INFO] Task started: fastANI
[2024-01-24 10:56:57,070] [INFO] Running command: fastANI --query /var/lib/cwl/stge2c28020-7f3d-4141-978d-8e0031dbf1c4/GCF_025369935.1_ASM2536993v1_genomic.fna.gz --refList GCF_025369935.1_ASM2536993v1_genomic.fna/target_genomes.txt --output GCF_025369935.1_ASM2536993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:09,837] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:09,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdccc90b3-0fae-4eb2-b008-d3a5494c411d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:09,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdccc90b3-0fae-4eb2-b008-d3a5494c411d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:09,847] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:09,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:09,848] [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 phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	91.1633	1803	2546	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	91.1232	1866	2546	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	91.0749	1680	2546	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	91.0471	1725	2546	95	below_threshold
Paenibacillus alginolyticus	strain=NBRC 15375	GCA_004000725.1	59839	59839	type	True	91.0032	1677	2546	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	77.7519	162	2546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:09,849] [INFO] DFAST Taxonomy check result was written to GCF_025369935.1_ASM2536993v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:09,850] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:09,850] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:09,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdccc90b3-0fae-4eb2-b008-d3a5494c411d/dqc_reference/checkm_data
[2024-01-24 10:57:09,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:09,924] [INFO] Task started: CheckM
[2024-01-24 10:57:09,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025369935.1_ASM2536993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025369935.1_ASM2536993v1_genomic.fna/checkm_input GCF_025369935.1_ASM2536993v1_genomic.fna/checkm_result
[2024-01-24 10:58:08,787] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:08,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:08,813] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:08,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:08,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025369935.1_ASM2536993v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:08,814] [INFO] Task started: Blastn
[2024-01-24 10:58:08,814] [INFO] Running command: blastn -query GCF_025369935.1_ASM2536993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdccc90b3-0fae-4eb2-b008-d3a5494c411d/dqc_reference/reference_markers_gtdb.fasta -out GCF_025369935.1_ASM2536993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:09,630] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:09,633] [INFO] Selected 5 target genomes.
[2024-01-24 10:58:09,634] [INFO] Target genome list was writen to GCF_025369935.1_ASM2536993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:09,638] [INFO] Task started: fastANI
[2024-01-24 10:58:09,638] [INFO] Running command: fastANI --query /var/lib/cwl/stge2c28020-7f3d-4141-978d-8e0031dbf1c4/GCF_025369935.1_ASM2536993v1_genomic.fna.gz --refList GCF_025369935.1_ASM2536993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025369935.1_ASM2536993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:20,755] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:20,764] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:20,765] [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_000799595.1	s__Paenibacillus_E chondroitinus_A	92.1062	1797	2546	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_001429545.1	s__Paenibacillus_E sp001429545	91.8552	1705	2546	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_013141715.1	s__Paenibacillus_E phytorum	91.1393	1806	2546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	95.60	95.60	0.80	0.80	2	-
GCF_000422905.1	s__Paenibacillus_E alginolyticus	91.0552	1724	2546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.46	96.94	0.87	0.75	3	-
GCF_001426375.1	s__Paenibacillus_E sp001426375	90.9902	1904	2546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.92	98.92	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:20,766] [INFO] GTDB search result was written to GCF_025369935.1_ASM2536993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:20,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:20,769] [INFO] DFAST_QC result json was written to GCF_025369935.1_ASM2536993v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:20,770] [INFO] DFAST_QC completed!
[2024-01-24 10:58:20,770] [INFO] Total running time: 0h1m46s