[2024-01-24 15:18:26,670] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:26,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:26,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg5751550c-9938-46d8-8290-108eb398587e/dqc_reference
[2024-01-24 15:18:27,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:27,997] [INFO] Task started: Prodigal
[2024-01-24 15:18:27,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg25b89290-5593-4559-89b7-896a9da24fd0/GCF_010994055.1_ASM1099405v1_genomic.fna.gz | prodigal -d GCF_010994055.1_ASM1099405v1_genomic.fna/cds.fna -a GCF_010994055.1_ASM1099405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:36,383] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:36,383] [INFO] Task started: HMMsearch
[2024-01-24 15:18:36,383] [INFO] Running command: hmmsearch --tblout GCF_010994055.1_ASM1099405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5751550c-9938-46d8-8290-108eb398587e/dqc_reference/reference_markers.hmm GCF_010994055.1_ASM1099405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:36,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:36,813] [INFO] Found 6/6 markers.
[2024-01-24 15:18:36,855] [INFO] Query marker FASTA was written to GCF_010994055.1_ASM1099405v1_genomic.fna/markers.fasta
[2024-01-24 15:18:36,856] [INFO] Task started: Blastn
[2024-01-24 15:18:36,856] [INFO] Running command: blastn -query GCF_010994055.1_ASM1099405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5751550c-9938-46d8-8290-108eb398587e/dqc_reference/reference_markers.fasta -out GCF_010994055.1_ASM1099405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:37,483] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:37,487] [INFO] Selected 14 target genomes.
[2024-01-24 15:18:37,487] [INFO] Target genome list was writen to GCF_010994055.1_ASM1099405v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:37,497] [INFO] Task started: fastANI
[2024-01-24 15:18:37,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg25b89290-5593-4559-89b7-896a9da24fd0/GCF_010994055.1_ASM1099405v1_genomic.fna.gz --refList GCF_010994055.1_ASM1099405v1_genomic.fna/target_genomes.txt --output GCF_010994055.1_ASM1099405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:50,779] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:50,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5751550c-9938-46d8-8290-108eb398587e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:50,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5751550c-9938-46d8-8290-108eb398587e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:50,797] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:18:50,798] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:18:50,798] [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 thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	100.0	1358	1363	95	inconclusive
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	99.99	1353	1363	95	inconclusive
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	96.1544	1148	1363	95	inconclusive
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	95.0276	1131	1363	95	inconclusive
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	91.3958	1069	1363	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	85.544	1012	1363	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	76.7256	55	1363	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.0856	55	1363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:50,801] [INFO] DFAST Taxonomy check result was written to GCF_010994055.1_ASM1099405v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:50,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:50,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:50,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5751550c-9938-46d8-8290-108eb398587e/dqc_reference/checkm_data
[2024-01-24 15:18:50,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:50,853] [INFO] Task started: CheckM
[2024-01-24 15:18:50,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010994055.1_ASM1099405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010994055.1_ASM1099405v1_genomic.fna/checkm_input GCF_010994055.1_ASM1099405v1_genomic.fna/checkm_result
[2024-01-24 15:19:22,725] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:22,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:22,749] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:22,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:22,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010994055.1_ASM1099405v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:22,750] [INFO] Task started: Blastn
[2024-01-24 15:19:22,751] [INFO] Running command: blastn -query GCF_010994055.1_ASM1099405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5751550c-9938-46d8-8290-108eb398587e/dqc_reference/reference_markers_gtdb.fasta -out GCF_010994055.1_ASM1099405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:23,554] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:23,558] [INFO] Selected 16 target genomes.
[2024-01-24 15:19:23,558] [INFO] Target genome list was writen to GCF_010994055.1_ASM1099405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:23,569] [INFO] Task started: fastANI
[2024-01-24 15:19:23,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg25b89290-5593-4559-89b7-896a9da24fd0/GCF_010994055.1_ASM1099405v1_genomic.fna.gz --refList GCF_010994055.1_ASM1099405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010994055.1_ASM1099405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:36,656] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:36,674] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:36,674] [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_000377765.1	s__Gracilibacillus lacisalsi	96.1544	1148	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	conclusive
GCF_017599345.1	s__Gracilibacillus sp017599345	91.4062	1068	1363	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_009650095.1	s__Gracilibacillus sp002797295	85.5483	1012	1363	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_900114645.1	s__Gracilibacillus orientalis	83.962	910	1363	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	79.1631	483	1363	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_900143085.1	s__Gracilibacillus kekensis	79.1416	456	1363	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	78.2023	370	1363	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_016909015.1	s__Gracilibacillus alcaliphilus	77.9087	231	1363	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_007301515.1	s__Radiobacillus deserti	77.3685	101	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	76.1156	54	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:36,676] [INFO] GTDB search result was written to GCF_010994055.1_ASM1099405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:36,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:36,682] [INFO] DFAST_QC result json was written to GCF_010994055.1_ASM1099405v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:36,683] [INFO] DFAST_QC completed!
[2024-01-24 15:19:36,683] [INFO] Total running time: 0h1m10s