[2024-01-24 13:41:20,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgc848419e-71e3-4292-a24b-e78607fb320d/dqc_reference
[2024-01-24 13:41:21,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,785] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b35d134-fc52-4fa6-9d28-275c1e29b434/GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna.gz | prodigal -d GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/cds.fna -a GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:27,418] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:27,418] [INFO] Task started: HMMsearch
[2024-01-24 13:41:27,418] [INFO] Running command: hmmsearch --tblout GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc848419e-71e3-4292-a24b-e78607fb320d/dqc_reference/reference_markers.hmm GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:27,704] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:27,705] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b35d134-fc52-4fa6-9d28-275c1e29b434/GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna.gz]
[2024-01-24 13:41:27,729] [INFO] Query marker FASTA was written to GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/markers.fasta
[2024-01-24 13:41:27,729] [INFO] Task started: Blastn
[2024-01-24 13:41:27,729] [INFO] Running command: blastn -query GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgc848419e-71e3-4292-a24b-e78607fb320d/dqc_reference/reference_markers.fasta -out GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:28,302] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:28,306] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:28,306] [INFO] Target genome list was writen to GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/target_genomes.txt
[2024-01-24 13:41:28,313] [INFO] Task started: fastANI
[2024-01-24 13:41:28,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b35d134-fc52-4fa6-9d28-275c1e29b434/GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna.gz --refList GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/target_genomes.txt --output GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:40,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:40,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc848419e-71e3-4292-a24b-e78607fb320d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:40,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc848419e-71e3-4292-a24b-e78607fb320d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:40,640] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:40,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:40,641] [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 kwashiorkori	strain=SIT6	GCA_001375515.1	1522318	1522318	type	True	100.0	920	920	95	conclusive
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	77.8589	128	920	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	77.6853	63	920	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	77.4385	63	920	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	77.0001	60	920	95	below_threshold
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	76.9669	50	920	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	76.9636	60	920	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	76.8988	55	920	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.6917	55	920	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	76.4712	58	920	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.2843	58	920	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	76.145	56	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:40,642] [INFO] DFAST Taxonomy check result was written to GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/tc_result.tsv
[2024-01-24 13:41:40,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:40,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:40,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc848419e-71e3-4292-a24b-e78607fb320d/dqc_reference/checkm_data
[2024-01-24 13:41:40,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:40,686] [INFO] Task started: CheckM
[2024-01-24 13:41:40,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/checkm_input GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/checkm_result
[2024-01-24 13:42:03,964] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:03,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,988] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:03,989] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:03,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/markers.fasta)
[2024-01-24 13:42:03,990] [INFO] Task started: Blastn
[2024-01-24 13:42:03,990] [INFO] Running command: blastn -query GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgc848419e-71e3-4292-a24b-e78607fb320d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:04,767] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:04,771] [INFO] Selected 19 target genomes.
[2024-01-24 13:42:04,771] [INFO] Target genome list was writen to GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:04,784] [INFO] Task started: fastANI
[2024-01-24 13:42:04,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b35d134-fc52-4fa6-9d28-275c1e29b434/GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna.gz --refList GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:18,446] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:18,461] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:18,461] [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_001375515.1	s__Bacillus_BK kwashiorkori	100.0	920	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_BK	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001244735.1	s__Bacillus_J andreraoultii	77.8	129	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_001420715.1	s__Margalitia shackletonii	77.6853	63	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	77.5787	67	920	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_016772275.1	s__Heyndrickxia vini	77.4385	63	920	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	-
GCF_002250055.1	s__Sutcliffiella cohnii	77.2301	62	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	77.2136	61	920	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_003259935.1	s__Anoxybacillus_B vitaminiphilus	76.9622	50	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829255.1	s__Metabacillus niabensis	76.6304	50	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_016908495.1	s__Bacillus_BW pakistanensis	76.4779	59	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BW	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844575.1	s__Margalitia camelliae	76.2843	58	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
GCF_002584535.1	s__Bacillus_A cereus_AW	76.1448	51	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:18,462] [INFO] GTDB search result was written to GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:18,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:18,466] [INFO] DFAST_QC result json was written to GCF_001375515.1_Rubiinfantum_massiliensis_genomic.fna/dqc_result.json
[2024-01-24 13:42:18,466] [INFO] DFAST_QC completed!
[2024-01-24 13:42:18,466] [INFO] Total running time: 0h0m58s