[2024-01-24 12:21:44,627] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bccdb97-f3c6-4c94-8b2e-c3d9db3b1a6e/dqc_reference
[2024-01-24 12:21:46,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,010] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg959a750a-65e5-4327-9949-0ae6803097b5/GCF_016908955.1_ASM1690895v1_genomic.fna.gz | prodigal -d GCF_016908955.1_ASM1690895v1_genomic.fna/cds.fna -a GCF_016908955.1_ASM1690895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:54,368] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:54,369] [INFO] Task started: HMMsearch
[2024-01-24 12:21:54,369] [INFO] Running command: hmmsearch --tblout GCF_016908955.1_ASM1690895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bccdb97-f3c6-4c94-8b2e-c3d9db3b1a6e/dqc_reference/reference_markers.hmm GCF_016908955.1_ASM1690895v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:54,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:54,759] [INFO] Found 6/6 markers.
[2024-01-24 12:21:54,806] [INFO] Query marker FASTA was written to GCF_016908955.1_ASM1690895v1_genomic.fna/markers.fasta
[2024-01-24 12:21:54,809] [INFO] Task started: Blastn
[2024-01-24 12:21:54,810] [INFO] Running command: blastn -query GCF_016908955.1_ASM1690895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bccdb97-f3c6-4c94-8b2e-c3d9db3b1a6e/dqc_reference/reference_markers.fasta -out GCF_016908955.1_ASM1690895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:55,554] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:55,558] [INFO] Selected 21 target genomes.
[2024-01-24 12:21:55,558] [INFO] Target genome list was writen to GCF_016908955.1_ASM1690895v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:55,566] [INFO] Task started: fastANI
[2024-01-24 12:21:55,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg959a750a-65e5-4327-9949-0ae6803097b5/GCF_016908955.1_ASM1690895v1_genomic.fna.gz --refList GCF_016908955.1_ASM1690895v1_genomic.fna/target_genomes.txt --output GCF_016908955.1_ASM1690895v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:11,700] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:11,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bccdb97-f3c6-4c94-8b2e-c3d9db3b1a6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:11,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bccdb97-f3c6-4c94-8b2e-c3d9db3b1a6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:11,716] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:11,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:11,717] [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=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	100.0	1409	1410	95	conclusive
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	99.9932	1405	1410	95	conclusive
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	77.971	252	1410	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.5458	149	1410	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	77.322	68	1410	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	77.1791	69	1410	95	below_threshold
Priestia filamentosa	strain=DSM 27955	GCA_002237735.1	1402861	1402861	type	True	77.0993	66	1410	95	below_threshold
Priestia filamentosa	strain=SGD-14	GCA_900177535.1	1402861	1402861	type	True	77.0993	66	1410	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.0827	124	1410	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.0523	93	1410	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	77.0511	52	1410	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.0326	70	1410	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.9258	77	1410	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	76.8107	122	1410	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.7617	111	1410	95	below_threshold
Priestia taiwanensis	strain=CGMCC 1.12698	GCA_014638355.1	1347902	1347902	type	True	76.7422	63	1410	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.6947	78	1410	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	76.5674	84	1410	95	below_threshold
Priestia taiwanensis	strain=DSM 27845	GCA_016908755.1	1347902	1347902	type	True	76.4191	63	1410	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.3534	78	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:11,718] [INFO] DFAST Taxonomy check result was written to GCF_016908955.1_ASM1690895v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:11,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:11,719] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:11,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bccdb97-f3c6-4c94-8b2e-c3d9db3b1a6e/dqc_reference/checkm_data
[2024-01-24 12:22:11,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:11,784] [INFO] Task started: CheckM
[2024-01-24 12:22:11,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908955.1_ASM1690895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908955.1_ASM1690895v1_genomic.fna/checkm_input GCF_016908955.1_ASM1690895v1_genomic.fna/checkm_result
[2024-01-24 12:22:43,336] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:43,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:43,374] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:43,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:43,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908955.1_ASM1690895v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:43,376] [INFO] Task started: Blastn
[2024-01-24 12:22:43,376] [INFO] Running command: blastn -query GCF_016908955.1_ASM1690895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bccdb97-f3c6-4c94-8b2e-c3d9db3b1a6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908955.1_ASM1690895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:44,219] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:44,222] [INFO] Selected 25 target genomes.
[2024-01-24 12:22:44,223] [INFO] Target genome list was writen to GCF_016908955.1_ASM1690895v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:44,240] [INFO] Task started: fastANI
[2024-01-24 12:22:44,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg959a750a-65e5-4327-9949-0ae6803097b5/GCF_016908955.1_ASM1690895v1_genomic.fna.gz --refList GCF_016908955.1_ASM1690895v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908955.1_ASM1690895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:04,974] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:04,996] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:04,997] [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	99.9932	1405	1410	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	78.0608	244	1410	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	77.9798	250	1410	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_004358205.1	s__Neobacillus salipaludis	77.3996	68	1410	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	77.3787	65	1410	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_002128405.1	s__Gottfriedia solisilvae	77.2866	69	1410	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_014960805.1	s__Bacillus_BV sp014960805	77.2676	168	1410	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_002871465.1	s__Metabacillus sp002871465	77.1509	114	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_018343665.1	s__Cytobacillus sp018343665	77.139	78	1410	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_900177535.1	s__Bacillus_I filamentosa	77.1386	65	1410	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_003184905.1	s__Priestia sp003184905	77.1331	88	1410	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_003667825.1	s__Metabacillus litoralis_B	77.0871	123	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	77.0587	94	1410	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_902168435.1	s__Bacillus_BU marasmi	77.0328	71	1410	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_009720625.1	s__Metabacillus sp004801455	77.0146	105	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	76.9408	89	1410	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_014217835.1	s__Metabacillus litoralis_A	76.8569	135	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_002734215.1	s__Fredinandcohnia onubensis	76.8309	121	1410	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_000518865.1	s__Metabacillus sp000518865	76.8101	128	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006384875.1	s__Bacillus_A bombysepticus	76.7822	77	1410	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_001591585.1	s__Niallia circulans	76.7812	79	1410	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	76.7789	64	1410	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	-
GCF_017874625.1	s__Cytobacillus eiseniae	76.5471	85	1410	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	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.3905	84	1410	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	-
GCA_011524525.1	s__Robertmurraya sp011524525	76.0589	66	1410	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,999] [INFO] GTDB search result was written to GCF_016908955.1_ASM1690895v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:05,000] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:05,005] [INFO] DFAST_QC result json was written to GCF_016908955.1_ASM1690895v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:05,006] [INFO] DFAST_QC completed!
[2024-01-24 12:23:05,006] [INFO] Total running time: 0h1m20s