[2024-01-24 14:19:18,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,987] [INFO] DQC Reference Directory: /var/lib/cwl/stge5912c58-bc6f-486f-a56a-e58fb3c64f59/dqc_reference
[2024-01-24 14:19:20,328] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,329] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,329] [INFO] Running command: gunzip -c /var/lib/cwl/stgabb32d0f-0673-46c5-8da7-cd50020456a6/GCF_011008845.1_ASM1100884v1_genomic.fna.gz | prodigal -d GCF_011008845.1_ASM1100884v1_genomic.fna/cds.fna -a GCF_011008845.1_ASM1100884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:28,487] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:28,487] [INFO] Task started: HMMsearch
[2024-01-24 14:19:28,487] [INFO] Running command: hmmsearch --tblout GCF_011008845.1_ASM1100884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5912c58-bc6f-486f-a56a-e58fb3c64f59/dqc_reference/reference_markers.hmm GCF_011008845.1_ASM1100884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:28,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:28,841] [INFO] Found 6/6 markers.
[2024-01-24 14:19:28,882] [INFO] Query marker FASTA was written to GCF_011008845.1_ASM1100884v1_genomic.fna/markers.fasta
[2024-01-24 14:19:28,883] [INFO] Task started: Blastn
[2024-01-24 14:19:28,883] [INFO] Running command: blastn -query GCF_011008845.1_ASM1100884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5912c58-bc6f-486f-a56a-e58fb3c64f59/dqc_reference/reference_markers.fasta -out GCF_011008845.1_ASM1100884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:29,634] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:29,637] [INFO] Selected 21 target genomes.
[2024-01-24 14:19:29,637] [INFO] Target genome list was writen to GCF_011008845.1_ASM1100884v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:29,645] [INFO] Task started: fastANI
[2024-01-24 14:19:29,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgabb32d0f-0673-46c5-8da7-cd50020456a6/GCF_011008845.1_ASM1100884v1_genomic.fna.gz --refList GCF_011008845.1_ASM1100884v1_genomic.fna/target_genomes.txt --output GCF_011008845.1_ASM1100884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:46,537] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:46,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5912c58-bc6f-486f-a56a-e58fb3c64f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:46,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5912c58-bc6f-486f-a56a-e58fb3c64f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:46,559] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:46,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:46,559] [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
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	100.0	1406	1408	95	conclusive
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	99.9959	1402	1408	95	conclusive
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	77.9466	240	1408	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.4456	150	1408	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.2711	67	1408	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	76.9982	116	1408	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.9757	126	1408	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.9548	73	1408	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.9269	74	1408	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.8704	108	1408	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.8288	101	1408	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	76.7861	75	1408	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.5657	79	1408	95	below_threshold
Priestia filamentosa	strain=SGD-14	GCA_900177535.1	1402861	1402861	type	True	76.5558	77	1408	95	below_threshold
Priestia filamentosa	strain=DSM 27955	GCA_002237735.1	1402861	1402861	type	True	76.5558	77	1408	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.4776	84	1408	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.4764	58	1408	95	below_threshold
Priestia taiwanensis	strain=CGMCC 1.12698	GCA_014638355.1	1347902	1347902	type	True	76.4011	63	1408	95	below_threshold
Priestia taiwanensis	strain=DSM 27845	GCA_016908755.1	1347902	1347902	type	True	76.4001	62	1408	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	75.9992	87	1408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:46,561] [INFO] DFAST Taxonomy check result was written to GCF_011008845.1_ASM1100884v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:46,561] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:46,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:46,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5912c58-bc6f-486f-a56a-e58fb3c64f59/dqc_reference/checkm_data
[2024-01-24 14:19:46,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:46,606] [INFO] Task started: CheckM
[2024-01-24 14:19:46,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011008845.1_ASM1100884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011008845.1_ASM1100884v1_genomic.fna/checkm_input GCF_011008845.1_ASM1100884v1_genomic.fna/checkm_result
[2024-01-24 14:20:17,415] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:17,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,439] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:17,439] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:17,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011008845.1_ASM1100884v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:17,440] [INFO] Task started: Blastn
[2024-01-24 14:20:17,440] [INFO] Running command: blastn -query GCF_011008845.1_ASM1100884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5912c58-bc6f-486f-a56a-e58fb3c64f59/dqc_reference/reference_markers_gtdb.fasta -out GCF_011008845.1_ASM1100884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:18,266] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:18,269] [INFO] Selected 25 target genomes.
[2024-01-24 14:20:18,269] [INFO] Target genome list was writen to GCF_011008845.1_ASM1100884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:18,284] [INFO] Task started: fastANI
[2024-01-24 14:20:18,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgabb32d0f-0673-46c5-8da7-cd50020456a6/GCF_011008845.1_ASM1100884v1_genomic.fna.gz --refList GCF_011008845.1_ASM1100884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011008845.1_ASM1100884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:37,626] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:37,654] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:37,655] [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_011008845.1	s__Bacillus_BS mesophilus	100.0	1406	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_008364785.1	s__Bacillus_BS sp008364785	77.9156	254	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016890225.1	s__Bacillus_BS sp016890225	77.9118	240	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902168435.1	s__Bacillus_BU marasmi	77.3049	67	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014960805.1	s__Bacillus_BV sp014960805	77.2989	174	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358205.1	s__Neobacillus salipaludis	77.1827	65	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860255.1	s__Neobacillus cucumis_A	77.1249	70	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667825.1	s__Metabacillus litoralis_B	77.0613	123	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_018343665.1	s__Cytobacillus sp018343665	77.056	83	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734215.1	s__Fredinandcohnia onubensis	76.9982	116	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003184905.1	s__Priestia sp003184905	76.9818	92	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720625.1	s__Metabacillus sp004801455	76.9593	100	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002871465.1	s__Metabacillus sp002871465	76.9329	122	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_002128405.1	s__Gottfriedia solisilvae	76.9269	74	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.14	96.28	0.93	0.87	3	-
GCF_014217835.1	s__Metabacillus litoralis_A	76.891	129	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	76.8514	99	1408	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	-
GCF_017874625.1	s__Cytobacillus eiseniae	76.7882	76	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	76.7096	95	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006384875.1	s__Bacillus_A bombysepticus	76.7079	81	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	97.0513	98.50	97.53	0.88	0.81	586	-
GCF_000518865.1	s__Metabacillus sp000518865	76.5858	139	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177535.1	s__Bacillus_I filamentosa	76.5834	76	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_I	95.0	99.55	98.90	0.95	0.92	6	-
GCF_001591585.1	s__Niallia circulans	76.5455	80	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.18	98.58	0.93	0.91	9	-
GCF_014638355.1	s__Priestia_D taiwanensis	76.3999	63	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Priestia_D	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011524525.1	s__Robertmurraya sp011524525	76.3896	58	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.2268	81	1408	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:37,656] [INFO] GTDB search result was written to GCF_011008845.1_ASM1100884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:37,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:37,662] [INFO] DFAST_QC result json was written to GCF_011008845.1_ASM1100884v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:37,662] [INFO] DFAST_QC completed!
[2024-01-24 14:20:37,662] [INFO] Total running time: 0h1m19s