[2024-01-25 20:13:35,373] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg85c8efdd-f69c-444b-a87f-24ecebaed74a/dqc_reference
[2024-01-25 20:13:36,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:36,516] [INFO] Task started: Prodigal
[2024-01-25 20:13:36,516] [INFO] Running command: gunzip -c /var/lib/cwl/stg12ce6844-80d6-4344-8443-a4d5d50c8d52/GCF_017873715.1_ASM1787371v1_genomic.fna.gz | prodigal -d GCF_017873715.1_ASM1787371v1_genomic.fna/cds.fna -a GCF_017873715.1_ASM1787371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:43,583] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:43,584] [INFO] Task started: HMMsearch
[2024-01-25 20:13:43,584] [INFO] Running command: hmmsearch --tblout GCF_017873715.1_ASM1787371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85c8efdd-f69c-444b-a87f-24ecebaed74a/dqc_reference/reference_markers.hmm GCF_017873715.1_ASM1787371v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:43,814] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:43,815] [INFO] Found 6/6 markers.
[2024-01-25 20:13:43,852] [INFO] Query marker FASTA was written to GCF_017873715.1_ASM1787371v1_genomic.fna/markers.fasta
[2024-01-25 20:13:43,852] [INFO] Task started: Blastn
[2024-01-25 20:13:43,852] [INFO] Running command: blastn -query GCF_017873715.1_ASM1787371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85c8efdd-f69c-444b-a87f-24ecebaed74a/dqc_reference/reference_markers.fasta -out GCF_017873715.1_ASM1787371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:44,417] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:44,420] [INFO] Selected 17 target genomes.
[2024-01-25 20:13:44,420] [INFO] Target genome list was writen to GCF_017873715.1_ASM1787371v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:44,431] [INFO] Task started: fastANI
[2024-01-25 20:13:44,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ce6844-80d6-4344-8443-a4d5d50c8d52/GCF_017873715.1_ASM1787371v1_genomic.fna.gz --refList GCF_017873715.1_ASM1787371v1_genomic.fna/target_genomes.txt --output GCF_017873715.1_ASM1787371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:59,455] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:59,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85c8efdd-f69c-444b-a87f-24ecebaed74a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:59,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85c8efdd-f69c-444b-a87f-24ecebaed74a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:59,467] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:13:59,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:59,467] [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
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	100.0	1402	1402	95	conclusive
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	99.9914	1386	1402	95	conclusive
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.7371	92	1402	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.668	215	1402	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.6649	239	1402	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	77.1832	152	1402	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.1019	131	1402	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.9337	153	1402	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	76.9236	170	1402	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	76.8825	98	1402	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	76.8663	156	1402	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.7798	52	1402	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	76.6483	108	1402	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.4858	95	1402	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.4796	101	1402	95	below_threshold
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	76.46	86	1402	95	below_threshold
Bacillus zhangzhouensis	strain=DW5-4	GCA_000715205.1	1178540	1178540	type	True	76.4147	64	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:59,468] [INFO] DFAST Taxonomy check result was written to GCF_017873715.1_ASM1787371v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:59,469] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:59,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:59,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85c8efdd-f69c-444b-a87f-24ecebaed74a/dqc_reference/checkm_data
[2024-01-25 20:13:59,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:59,513] [INFO] Task started: CheckM
[2024-01-25 20:13:59,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873715.1_ASM1787371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873715.1_ASM1787371v1_genomic.fna/checkm_input GCF_017873715.1_ASM1787371v1_genomic.fna/checkm_result
[2024-01-25 20:14:25,967] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:25,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:25,987] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:25,987] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:25,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873715.1_ASM1787371v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:25,988] [INFO] Task started: Blastn
[2024-01-25 20:14:25,989] [INFO] Running command: blastn -query GCF_017873715.1_ASM1787371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85c8efdd-f69c-444b-a87f-24ecebaed74a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873715.1_ASM1787371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:26,780] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:26,784] [INFO] Selected 18 target genomes.
[2024-01-25 20:14:26,784] [INFO] Target genome list was writen to GCF_017873715.1_ASM1787371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:26,794] [INFO] Task started: fastANI
[2024-01-25 20:14:26,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ce6844-80d6-4344-8443-a4d5d50c8d52/GCF_017873715.1_ASM1787371v1_genomic.fna.gz --refList GCF_017873715.1_ASM1787371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873715.1_ASM1787371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:42,717] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:42,728] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:42,728] [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_017873715.1	s__Bacillus_BV luteolus	100.0	1402	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014960805.1	s__Bacillus_BV sp014960805	89.5978	1186	1402	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_002019645.1	s__Litchfieldia alkalitelluris	77.668	215	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003400205.1	s__Fredinandcohnia sp003400205	77.6526	173	1402	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_900104555.1	s__Litchfieldia salsa	77.6485	239	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	77.6269	176	1402	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_001439915.1	s__Fredinandcohnia humi	77.6026	161	1402	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_004799755.1	s__Fredinandcohnia timonensis_A	77.3005	184	1402	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_000285535.1	s__Fredinandcohnia timonensis	77.1806	175	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908835.1	s__Bacillus_AD endoradicis	77.0685	109	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482325.1	s__Neobacillus sp000482325	77.0285	113	1402	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_017497975.1	s__Metabacillus sp017497975	76.9209	154	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917645.1	s__Robertmurraya sp009917645	76.9157	131	1402	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	-
GCF_003667825.1	s__Metabacillus litoralis_B	76.8271	168	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_000686805.1	s__Neobacillus sp000686805	76.7413	102	1402	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_002577655.1	s__Metabacillus sp002577655	76.6576	157	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591565.1	s__Priestia flexa	76.5666	122	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCF_000518865.1	s__Metabacillus sp000518865	76.5558	146	1402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:42,731] [INFO] GTDB search result was written to GCF_017873715.1_ASM1787371v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:42,731] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:42,735] [INFO] DFAST_QC result json was written to GCF_017873715.1_ASM1787371v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:42,735] [INFO] DFAST_QC completed!
[2024-01-25 20:14:42,735] [INFO] Total running time: 0h1m7s