[2024-01-24 12:44:33,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:33,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:33,824] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0d9305d-d58e-4eae-a15e-e9de0cf12b0a/dqc_reference
[2024-01-24 12:44:34,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:34,944] [INFO] Task started: Prodigal
[2024-01-24 12:44:34,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d4f71f4-a81a-4024-a360-7038eafcd748/GCF_018998565.1_ASM1899856v1_genomic.fna.gz | prodigal -d GCF_018998565.1_ASM1899856v1_genomic.fna/cds.fna -a GCF_018998565.1_ASM1899856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:56,252] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:56,252] [INFO] Task started: HMMsearch
[2024-01-24 12:44:56,253] [INFO] Running command: hmmsearch --tblout GCF_018998565.1_ASM1899856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0d9305d-d58e-4eae-a15e-e9de0cf12b0a/dqc_reference/reference_markers.hmm GCF_018998565.1_ASM1899856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:56,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:56,559] [INFO] Found 6/6 markers.
[2024-01-24 12:44:56,618] [INFO] Query marker FASTA was written to GCF_018998565.1_ASM1899856v1_genomic.fna/markers.fasta
[2024-01-24 12:44:56,619] [INFO] Task started: Blastn
[2024-01-24 12:44:56,619] [INFO] Running command: blastn -query GCF_018998565.1_ASM1899856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0d9305d-d58e-4eae-a15e-e9de0cf12b0a/dqc_reference/reference_markers.fasta -out GCF_018998565.1_ASM1899856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:57,231] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:57,235] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:57,236] [INFO] Target genome list was writen to GCF_018998565.1_ASM1899856v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:57,265] [INFO] Task started: fastANI
[2024-01-24 12:44:57,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d4f71f4-a81a-4024-a360-7038eafcd748/GCF_018998565.1_ASM1899856v1_genomic.fna.gz --refList GCF_018998565.1_ASM1899856v1_genomic.fna/target_genomes.txt --output GCF_018998565.1_ASM1899856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:13,242] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:13,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0d9305d-d58e-4eae-a15e-e9de0cf12b0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:13,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0d9305d-d58e-4eae-a15e-e9de0cf12b0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:13,253] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:13,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:13,254] [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 elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	93.5121	2088	2576	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	93.0115	2041	2576	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	91.3795	1559	2576	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	91.309	1990	2576	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	78.91	507	2576	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	78.6601	446	2576	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	78.268	376	2576	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.2509	150	2576	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.0277	206	2576	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.8706	125	2576	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.7938	130	2576	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	75.7266	117	2576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:13,255] [INFO] DFAST Taxonomy check result was written to GCF_018998565.1_ASM1899856v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:13,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:13,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:13,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0d9305d-d58e-4eae-a15e-e9de0cf12b0a/dqc_reference/checkm_data
[2024-01-24 12:45:13,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:13,328] [INFO] Task started: CheckM
[2024-01-24 12:45:13,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018998565.1_ASM1899856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018998565.1_ASM1899856v1_genomic.fna/checkm_input GCF_018998565.1_ASM1899856v1_genomic.fna/checkm_result
[2024-01-24 12:46:14,257] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:14,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:14,283] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:14,283] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:14,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018998565.1_ASM1899856v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:14,283] [INFO] Task started: Blastn
[2024-01-24 12:46:14,284] [INFO] Running command: blastn -query GCF_018998565.1_ASM1899856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0d9305d-d58e-4eae-a15e-e9de0cf12b0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_018998565.1_ASM1899856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:15,090] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:15,094] [INFO] Selected 7 target genomes.
[2024-01-24 12:46:15,094] [INFO] Target genome list was writen to GCF_018998565.1_ASM1899856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:15,127] [INFO] Task started: fastANI
[2024-01-24 12:46:15,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d4f71f4-a81a-4024-a360-7038eafcd748/GCF_018998565.1_ASM1899856v1_genomic.fna.gz --refList GCF_018998565.1_ASM1899856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018998565.1_ASM1899856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:27,058] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:27,064] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:27,064] [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_018998565.1	s__Paenibacillus_G sp018998565	100.0	2569	2576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001399685.1	s__Paenibacillus_G sp001399685	93.7126	2014	2576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000865.1	s__Paenibacillus_G elgii	93.5119	2088	2576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	92.9875	2044	2576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
GCF_900100345.1	s__Paenibacillus_G tianmuensis	91.3795	1559	2576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000785.1	s__Paenibacillus_G ehimensis	91.2894	1993	2576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:27,066] [INFO] GTDB search result was written to GCF_018998565.1_ASM1899856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:27,066] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:27,069] [INFO] DFAST_QC result json was written to GCF_018998565.1_ASM1899856v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:27,070] [INFO] DFAST_QC completed!
[2024-01-24 12:46:27,070] [INFO] Total running time: 0h1m53s