[2024-01-25 19:57:35,674] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:35,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:35,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ff7d736-7489-4ed1-a26d-31233cae4850/dqc_reference
[2024-01-25 19:57:36,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:36,846] [INFO] Task started: Prodigal
[2024-01-25 19:57:36,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg154e35bd-2870-4a5e-9bde-434ed35a4174/GCF_009882985.1_ASM988298v1_genomic.fna.gz | prodigal -d GCF_009882985.1_ASM988298v1_genomic.fna/cds.fna -a GCF_009882985.1_ASM988298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:55,414] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:55,414] [INFO] Task started: HMMsearch
[2024-01-25 19:57:55,414] [INFO] Running command: hmmsearch --tblout GCF_009882985.1_ASM988298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ff7d736-7489-4ed1-a26d-31233cae4850/dqc_reference/reference_markers.hmm GCF_009882985.1_ASM988298v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:55,809] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:55,810] [INFO] Found 6/6 markers.
[2024-01-25 19:57:55,873] [INFO] Query marker FASTA was written to GCF_009882985.1_ASM988298v1_genomic.fna/markers.fasta
[2024-01-25 19:57:55,873] [INFO] Task started: Blastn
[2024-01-25 19:57:55,873] [INFO] Running command: blastn -query GCF_009882985.1_ASM988298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ff7d736-7489-4ed1-a26d-31233cae4850/dqc_reference/reference_markers.fasta -out GCF_009882985.1_ASM988298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:56,429] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:56,432] [INFO] Selected 8 target genomes.
[2024-01-25 19:57:56,432] [INFO] Target genome list was writen to GCF_009882985.1_ASM988298v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:56,436] [INFO] Task started: fastANI
[2024-01-25 19:57:56,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg154e35bd-2870-4a5e-9bde-434ed35a4174/GCF_009882985.1_ASM988298v1_genomic.fna.gz --refList GCF_009882985.1_ASM988298v1_genomic.fna/target_genomes.txt --output GCF_009882985.1_ASM988298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:08,869] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:08,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ff7d736-7489-4ed1-a26d-31233cae4850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:08,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ff7d736-7489-4ed1-a26d-31233cae4850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:08,882] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:08,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:08,882] [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 silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	100.0	2706	2710	95	conclusive
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	88.0117	2134	2710	95	below_threshold
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	87.9201	1985	2710	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	84.6101	1624	2710	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	84.0003	1486	2710	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.1103	133	2710	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	76.7834	55	2710	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:08,884] [INFO] DFAST Taxonomy check result was written to GCF_009882985.1_ASM988298v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:08,884] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:08,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:08,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ff7d736-7489-4ed1-a26d-31233cae4850/dqc_reference/checkm_data
[2024-01-25 19:58:08,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:08,959] [INFO] Task started: CheckM
[2024-01-25 19:58:08,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009882985.1_ASM988298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009882985.1_ASM988298v1_genomic.fna/checkm_input GCF_009882985.1_ASM988298v1_genomic.fna/checkm_result
[2024-01-25 19:59:03,550] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:03,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:03,582] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:03,582] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:03,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009882985.1_ASM988298v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:03,583] [INFO] Task started: Blastn
[2024-01-25 19:59:03,583] [INFO] Running command: blastn -query GCF_009882985.1_ASM988298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ff7d736-7489-4ed1-a26d-31233cae4850/dqc_reference/reference_markers_gtdb.fasta -out GCF_009882985.1_ASM988298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:04,338] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:04,341] [INFO] Selected 5 target genomes.
[2024-01-25 19:59:04,341] [INFO] Target genome list was writen to GCF_009882985.1_ASM988298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:04,348] [INFO] Task started: fastANI
[2024-01-25 19:59:04,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg154e35bd-2870-4a5e-9bde-434ed35a4174/GCF_009882985.1_ASM988298v1_genomic.fna.gz --refList GCF_009882985.1_ASM988298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009882985.1_ASM988298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:15,817] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:15,821] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:15,821] [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_009882985.1	s__Paenibacillus_E silvestris	100.0	2706	2710	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	conclusive
GCF_007829615.1	s__Paenibacillus_E sp007829615	91.6342	2338	2710	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_004000765.1	s__Paenibacillus_E chondroitinus	87.9199	1985	2710	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	-
GCF_017874035.1	s__Paenibacillus_E aceris	84.5924	1627	2710	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	83.9939	1487	2710	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:15,823] [INFO] GTDB search result was written to GCF_009882985.1_ASM988298v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:15,823] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:15,825] [INFO] DFAST_QC result json was written to GCF_009882985.1_ASM988298v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:15,825] [INFO] DFAST_QC completed!
[2024-01-25 19:59:15,825] [INFO] Total running time: 0h1m40s