[2024-01-24 13:22:12,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:12,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:12,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg14b60e45-724e-4a06-bbea-faea6bf99c5b/dqc_reference
[2024-01-24 13:22:13,271] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,272] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg882dd125-b0d6-4f94-bfde-13b43cb00eb2/GCF_900086715.1_PRJEB13933_genomic.fna.gz | prodigal -d GCF_900086715.1_PRJEB13933_genomic.fna/cds.fna -a GCF_900086715.1_PRJEB13933_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:23,704] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:23,704] [INFO] Task started: HMMsearch
[2024-01-24 13:22:23,704] [INFO] Running command: hmmsearch --tblout GCF_900086715.1_PRJEB13933_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14b60e45-724e-4a06-bbea-faea6bf99c5b/dqc_reference/reference_markers.hmm GCF_900086715.1_PRJEB13933_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:24,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:24,092] [INFO] Found 6/6 markers.
[2024-01-24 13:22:24,132] [INFO] Query marker FASTA was written to GCF_900086715.1_PRJEB13933_genomic.fna/markers.fasta
[2024-01-24 13:22:24,132] [INFO] Task started: Blastn
[2024-01-24 13:22:24,133] [INFO] Running command: blastn -query GCF_900086715.1_PRJEB13933_genomic.fna/markers.fasta -db /var/lib/cwl/stg14b60e45-724e-4a06-bbea-faea6bf99c5b/dqc_reference/reference_markers.fasta -out GCF_900086715.1_PRJEB13933_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:24,784] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:24,788] [INFO] Selected 23 target genomes.
[2024-01-24 13:22:24,788] [INFO] Target genome list was writen to GCF_900086715.1_PRJEB13933_genomic.fna/target_genomes.txt
[2024-01-24 13:22:24,825] [INFO] Task started: fastANI
[2024-01-24 13:22:24,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg882dd125-b0d6-4f94-bfde-13b43cb00eb2/GCF_900086715.1_PRJEB13933_genomic.fna.gz --refList GCF_900086715.1_PRJEB13933_genomic.fna/target_genomes.txt --output GCF_900086715.1_PRJEB13933_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:44,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:44,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14b60e45-724e-4a06-bbea-faea6bf99c5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:44,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14b60e45-724e-4a06-bbea-faea6bf99c5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:44,100] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:44,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:44,100] [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	100.0	1510	1510	95	conclusive
Gracilibacillus massiliensis	strain=Awa-1	GCA_001458115.1	1564956	1564956	type	True	77.6453	207	1510	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.6169	189	1510	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	77.5457	193	1510	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	77.5208	63	1510	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	77.4388	63	1510	95	below_threshold
Gracilibacillus boraciitolerans	strain=JCM 21714	GCA_000521485.1	307521	307521	type	True	77.2686	143	1510	95	below_threshold
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	77.2569	182	1510	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.9076	59	1510	95	below_threshold
Pseudogracilibacillus auburnensis	strain=DSM 28556	GCA_003201975.1	1494959	1494959	type	True	76.4124	56	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:44,102] [INFO] DFAST Taxonomy check result was written to GCF_900086715.1_PRJEB13933_genomic.fna/tc_result.tsv
[2024-01-24 13:22:44,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:44,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:44,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14b60e45-724e-4a06-bbea-faea6bf99c5b/dqc_reference/checkm_data
[2024-01-24 13:22:44,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:44,154] [INFO] Task started: CheckM
[2024-01-24 13:22:44,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900086715.1_PRJEB13933_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900086715.1_PRJEB13933_genomic.fna/checkm_input GCF_900086715.1_PRJEB13933_genomic.fna/checkm_result
[2024-01-24 13:23:22,656] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:22,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:22,678] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:22,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:22,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900086715.1_PRJEB13933_genomic.fna/markers.fasta)
[2024-01-24 13:23:22,680] [INFO] Task started: Blastn
[2024-01-24 13:23:22,680] [INFO] Running command: blastn -query GCF_900086715.1_PRJEB13933_genomic.fna/markers.fasta -db /var/lib/cwl/stg14b60e45-724e-4a06-bbea-faea6bf99c5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900086715.1_PRJEB13933_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:23,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:23,496] [INFO] Selected 24 target genomes.
[2024-01-24 13:23:23,497] [INFO] Target genome list was writen to GCF_900086715.1_PRJEB13933_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:23,526] [INFO] Task started: fastANI
[2024-01-24 13:23:23,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg882dd125-b0d6-4f94-bfde-13b43cb00eb2/GCF_900086715.1_PRJEB13933_genomic.fna.gz --refList GCF_900086715.1_PRJEB13933_genomic.fna/target_genomes_gtdb.txt --output GCF_900086715.1_PRJEB13933_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:40,144] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:40,153] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:40,154] [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
GCA_900626275.1	s__Gracilibacillus phocaeensis	99.016	1346	1510	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.02	99.02	0.89	0.89	3	conclusive
GCF_016909015.1	s__Gracilibacillus alcaliphilus	78.1853	388	1510	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	77.6477	207	1510	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	77.5691	192	1510	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_017599345.1	s__Gracilibacillus sp017599345	77.5294	195	1510	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_003515705.1	s__Oceanobacillus profundus	77.4547	64	1510	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_010993965.1	s__Gracilibacillus sp010993965	77.3131	124	1510	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_000521485.1	s__Gracilibacillus boraciitolerans	77.2686	143	1510	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	77.2363	185	1510	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:40,156] [INFO] GTDB search result was written to GCF_900086715.1_PRJEB13933_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:40,156] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:40,160] [INFO] DFAST_QC result json was written to GCF_900086715.1_PRJEB13933_genomic.fna/dqc_result.json
[2024-01-24 13:23:40,161] [INFO] DFAST_QC completed!
[2024-01-24 13:23:40,161] [INFO] Total running time: 0h1m28s