[2024-01-24 10:47:06,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,557] [INFO] DQC Reference Directory: /var/lib/cwl/stgca8cc82f-c779-4e81-8145-abaf16313a71/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3ee3133-2e0a-4a02-91f4-385cf9e50a61/GCF_016909015.1_ASM1690901v1_genomic.fna.gz | prodigal -d GCF_016909015.1_ASM1690901v1_genomic.fna/cds.fna -a GCF_016909015.1_ASM1690901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,069] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,070] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,070] [INFO] Running command: hmmsearch --tblout GCF_016909015.1_ASM1690901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca8cc82f-c779-4e81-8145-abaf16313a71/dqc_reference/reference_markers.hmm GCF_016909015.1_ASM1690901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,406] [INFO] Found 6/6 markers.
[2024-01-24 10:47:23,445] [INFO] Query marker FASTA was written to GCF_016909015.1_ASM1690901v1_genomic.fna/markers.fasta
[2024-01-24 10:47:23,445] [INFO] Task started: Blastn
[2024-01-24 10:47:23,445] [INFO] Running command: blastn -query GCF_016909015.1_ASM1690901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca8cc82f-c779-4e81-8145-abaf16313a71/dqc_reference/reference_markers.fasta -out GCF_016909015.1_ASM1690901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:24,043] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:24,047] [INFO] Selected 22 target genomes.
[2024-01-24 10:47:24,047] [INFO] Target genome list was writen to GCF_016909015.1_ASM1690901v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:24,075] [INFO] Task started: fastANI
[2024-01-24 10:47:24,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ee3133-2e0a-4a02-91f4-385cf9e50a61/GCF_016909015.1_ASM1690901v1_genomic.fna.gz --refList GCF_016909015.1_ASM1690901v1_genomic.fna/target_genomes.txt --output GCF_016909015.1_ASM1690901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:40,151] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:40,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca8cc82f-c779-4e81-8145-abaf16313a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:40,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca8cc82f-c779-4e81-8145-abaf16313a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:40,160] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:40,160] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:40,161] [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
Gracilibacillus timonensis	strain=Marseille-P2481	GCA_900086715.1	1816696	1816696	type	True	78.2203	384	1682	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	78.0966	233	1682	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	78.057	230	1682	95	below_threshold
Amphibacillus sediminis	strain=NBRC 103570	GCA_001552275.1	360185	360185	type	True	77.9287	84	1682	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.7497	239	1682	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	77.6729	242	1682	95	below_threshold
Gracilibacillus boraciitolerans	strain=JCM 21714	GCA_000521485.1	307521	307521	type	True	77.6551	156	1682	95	below_threshold
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	77.6407	235	1682	95	below_threshold
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	77.5358	209	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:40,163] [INFO] DFAST Taxonomy check result was written to GCF_016909015.1_ASM1690901v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:40,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:40,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:40,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca8cc82f-c779-4e81-8145-abaf16313a71/dqc_reference/checkm_data
[2024-01-24 10:47:40,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:40,211] [INFO] Task started: CheckM
[2024-01-24 10:47:40,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016909015.1_ASM1690901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016909015.1_ASM1690901v1_genomic.fna/checkm_input GCF_016909015.1_ASM1690901v1_genomic.fna/checkm_result
[2024-01-24 10:48:16,025] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:16,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,049] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:16,050] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:16,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016909015.1_ASM1690901v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:16,050] [INFO] Task started: Blastn
[2024-01-24 10:48:16,050] [INFO] Running command: blastn -query GCF_016909015.1_ASM1690901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca8cc82f-c779-4e81-8145-abaf16313a71/dqc_reference/reference_markers_gtdb.fasta -out GCF_016909015.1_ASM1690901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:16,880] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:16,884] [INFO] Selected 20 target genomes.
[2024-01-24 10:48:16,884] [INFO] Target genome list was writen to GCF_016909015.1_ASM1690901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:16,931] [INFO] Task started: fastANI
[2024-01-24 10:48:16,931] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ee3133-2e0a-4a02-91f4-385cf9e50a61/GCF_016909015.1_ASM1690901v1_genomic.fna.gz --refList GCF_016909015.1_ASM1690901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016909015.1_ASM1690901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:31,601] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:31,612] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:31,612] [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_016909015.1	s__Gracilibacillus alcaliphilus	100.0	1678	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900626275.1	s__Gracilibacillus phocaeensis	78.2615	390	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.02	99.02	0.89	0.89	3	-
GCF_001552275.1	s__Amphibacillus_B sediminis	77.9287	84	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143085.1	s__Gracilibacillus kekensis	77.8604	197	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458115.1	s__Gracilibacillus massiliensis	77.8319	198	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000377765.1	s__Gracilibacillus lacisalsi	77.7761	237	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_009650095.1	s__Gracilibacillus sp002797295	77.6729	242	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_003176895.1	s__Gracilibacillus dipsosauri	77.6382	144	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	-
GCF_900111195.1	s__Gracilibacillus ureilyticus	77.6308	135	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114645.1	s__Gracilibacillus orientalis	77.5424	210	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498735.1	s__Gracilibacillus sp009498735	77.3463	157	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.0398	64	1682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:31,613] [INFO] GTDB search result was written to GCF_016909015.1_ASM1690901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:31,614] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:31,617] [INFO] DFAST_QC result json was written to GCF_016909015.1_ASM1690901v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:31,618] [INFO] DFAST_QC completed!
[2024-01-24 10:48:31,618] [INFO] Total running time: 0h1m25s