[2024-01-24 12:14:34,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg51bd54c9-29ae-4a65-903a-8d297a021db4/dqc_reference
[2024-01-24 12:14:35,458] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,458] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg65a1a910-a766-46bc-8033-91cf59935682/GCF_017599345.1_ASM1759934v1_genomic.fna.gz | prodigal -d GCF_017599345.1_ASM1759934v1_genomic.fna/cds.fna -a GCF_017599345.1_ASM1759934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:44,583] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:44,584] [INFO] Task started: HMMsearch
[2024-01-24 12:14:44,584] [INFO] Running command: hmmsearch --tblout GCF_017599345.1_ASM1759934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51bd54c9-29ae-4a65-903a-8d297a021db4/dqc_reference/reference_markers.hmm GCF_017599345.1_ASM1759934v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:44,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:44,850] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,889] [INFO] Query marker FASTA was written to GCF_017599345.1_ASM1759934v1_genomic.fna/markers.fasta
[2024-01-24 12:14:44,890] [INFO] Task started: Blastn
[2024-01-24 12:14:44,890] [INFO] Running command: blastn -query GCF_017599345.1_ASM1759934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51bd54c9-29ae-4a65-903a-8d297a021db4/dqc_reference/reference_markers.fasta -out GCF_017599345.1_ASM1759934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:45,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:45,506] [INFO] Selected 9 target genomes.
[2024-01-24 12:14:45,507] [INFO] Target genome list was writen to GCF_017599345.1_ASM1759934v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:45,512] [INFO] Task started: fastANI
[2024-01-24 12:14:45,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a1a910-a766-46bc-8033-91cf59935682/GCF_017599345.1_ASM1759934v1_genomic.fna.gz --refList GCF_017599345.1_ASM1759934v1_genomic.fna/target_genomes.txt --output GCF_017599345.1_ASM1759934v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:55,215] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:55,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51bd54c9-29ae-4a65-903a-8d297a021db4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:55,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51bd54c9-29ae-4a65-903a-8d297a021db4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:55,223] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:55,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:55,223] [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 suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	100.0	1515	1517	95	conclusive
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	91.4144	1186	1517	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	91.2461	1085	1517	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	91.2374	1098	1517	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	91.1806	1192	1517	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	85.5962	1137	1517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:55,225] [INFO] DFAST Taxonomy check result was written to GCF_017599345.1_ASM1759934v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:55,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:55,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:55,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51bd54c9-29ae-4a65-903a-8d297a021db4/dqc_reference/checkm_data
[2024-01-24 12:14:55,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:55,273] [INFO] Task started: CheckM
[2024-01-24 12:14:55,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017599345.1_ASM1759934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017599345.1_ASM1759934v1_genomic.fna/checkm_input GCF_017599345.1_ASM1759934v1_genomic.fna/checkm_result
[2024-01-24 12:15:27,921] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:27,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:27,947] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:27,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:27,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017599345.1_ASM1759934v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:27,947] [INFO] Task started: Blastn
[2024-01-24 12:15:27,948] [INFO] Running command: blastn -query GCF_017599345.1_ASM1759934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51bd54c9-29ae-4a65-903a-8d297a021db4/dqc_reference/reference_markers_gtdb.fasta -out GCF_017599345.1_ASM1759934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:28,740] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:28,743] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:28,744] [INFO] Target genome list was writen to GCF_017599345.1_ASM1759934v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:28,752] [INFO] Task started: fastANI
[2024-01-24 12:15:28,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a1a910-a766-46bc-8033-91cf59935682/GCF_017599345.1_ASM1759934v1_genomic.fna.gz --refList GCF_017599345.1_ASM1759934v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017599345.1_ASM1759934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:39,170] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:39,181] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:39,181] [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_017599345.1	s__Gracilibacillus sp017599345	100.0	1515	1517	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
GCF_000377765.1	s__Gracilibacillus lacisalsi	91.1725	1193	1517	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	85.5887	1138	1517	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	84.06	1034	1517	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	78.9679	503	1517	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_010993965.1	s__Gracilibacillus sp010993965	78.4673	287	1517	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	78.0816	378	1517	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900626275.1	s__Gracilibacillus phocaeensis	77.9888	186	1517	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_014083865.1	s__Paraliobacillus salinarum	77.3	89	1517	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908375.1	s__Amphibacillus_C cookii	76.9325	80	1517	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110345.1	s__Amphibacillus_D marinus	76.8365	59	1517	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:39,183] [INFO] GTDB search result was written to GCF_017599345.1_ASM1759934v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:39,183] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:39,188] [INFO] DFAST_QC result json was written to GCF_017599345.1_ASM1759934v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:39,188] [INFO] DFAST_QC completed!
[2024-01-24 12:15:39,188] [INFO] Total running time: 0h1m5s