[2024-01-24 14:21:50,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,962] [INFO] DQC Reference Directory: /var/lib/cwl/stga1bd115e-7443-4336-a12f-10e5f6afa0f1/dqc_reference
[2024-01-24 14:21:52,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,335] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d7f423e-7e91-4be5-83b1-a76e1271a5db/GCF_003570705.1_ASM357070v1_genomic.fna.gz | prodigal -d GCF_003570705.1_ASM357070v1_genomic.fna/cds.fna -a GCF_003570705.1_ASM357070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:03,483] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:03,484] [INFO] Task started: HMMsearch
[2024-01-24 14:22:03,484] [INFO] Running command: hmmsearch --tblout GCF_003570705.1_ASM357070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1bd115e-7443-4336-a12f-10e5f6afa0f1/dqc_reference/reference_markers.hmm GCF_003570705.1_ASM357070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:03,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:03,793] [INFO] Found 6/6 markers.
[2024-01-24 14:22:03,837] [INFO] Query marker FASTA was written to GCF_003570705.1_ASM357070v1_genomic.fna/markers.fasta
[2024-01-24 14:22:03,838] [INFO] Task started: Blastn
[2024-01-24 14:22:03,838] [INFO] Running command: blastn -query GCF_003570705.1_ASM357070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1bd115e-7443-4336-a12f-10e5f6afa0f1/dqc_reference/reference_markers.fasta -out GCF_003570705.1_ASM357070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:04,493] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:04,497] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:04,497] [INFO] Target genome list was writen to GCF_003570705.1_ASM357070v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:04,522] [INFO] Task started: fastANI
[2024-01-24 14:22:04,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d7f423e-7e91-4be5-83b1-a76e1271a5db/GCF_003570705.1_ASM357070v1_genomic.fna.gz --refList GCF_003570705.1_ASM357070v1_genomic.fna/target_genomes.txt --output GCF_003570705.1_ASM357070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:21,924] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:21,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1bd115e-7443-4336-a12f-10e5f6afa0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:21,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1bd115e-7443-4336-a12f-10e5f6afa0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:21,944] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:21,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:21,945] [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
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	100.0	1372	1376	95	conclusive
Mesobacillus zeae	strain=JJ-247	GCA_013618945.1	1917180	1917180	type	True	99.9991	1376	1376	95	conclusive
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.7084	123	1376	95	below_threshold
Mesobacillus harenae	strain=Y40	GCA_013343715.1	2213203	2213203	type	True	78.0611	139	1376	95	below_threshold
Mesobacillus subterraneus	strain=DSM 13966	GCA_003937825.1	285983	285983	suspected-type	True	77.9127	197	1376	95	below_threshold
Bacillus massiliglaciei	strain=Marseille-P2600	GCA_900098925.1	1816693	1816693	type	True	77.8158	65	1376	95	below_threshold
Mesobacillus foraminis	strain=CV53	GCA_013618915.1	279826	279826	type	True	77.7309	209	1376	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.694	94	1376	95	below_threshold
Mesobacillus foraminis	strain=CV53	GCA_004340465.1	279826	279826	type	True	77.6828	211	1376	95	below_threshold
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	77.6723	184	1376	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.595	122	1376	95	below_threshold
Peribacillus glennii	strain=V44-8	GCA_003429105.1	2303991	2303991	type	True	77.5549	83	1376	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.3758	67	1376	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.21	135	1376	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.1851	113	1376	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	77.0458	62	1376	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	77.0381	76	1376	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	77.0097	51	1376	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.9301	131	1376	95	below_threshold
Metabacillus kandeliae	strain=GX 13764	GCA_021166585.1	2900151	2900151	type	True	76.7218	73	1376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:21,947] [INFO] DFAST Taxonomy check result was written to GCF_003570705.1_ASM357070v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:21,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:21,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:21,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1bd115e-7443-4336-a12f-10e5f6afa0f1/dqc_reference/checkm_data
[2024-01-24 14:22:21,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:21,999] [INFO] Task started: CheckM
[2024-01-24 14:22:21,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003570705.1_ASM357070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003570705.1_ASM357070v1_genomic.fna/checkm_input GCF_003570705.1_ASM357070v1_genomic.fna/checkm_result
[2024-01-24 14:22:57,349] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:57,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:57,373] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:57,374] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:57,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003570705.1_ASM357070v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:57,374] [INFO] Task started: Blastn
[2024-01-24 14:22:57,375] [INFO] Running command: blastn -query GCF_003570705.1_ASM357070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1bd115e-7443-4336-a12f-10e5f6afa0f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003570705.1_ASM357070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:58,125] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:58,129] [INFO] Selected 26 target genomes.
[2024-01-24 14:22:58,129] [INFO] Target genome list was writen to GCF_003570705.1_ASM357070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:58,153] [INFO] Task started: fastANI
[2024-01-24 14:22:58,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d7f423e-7e91-4be5-83b1-a76e1271a5db/GCF_003570705.1_ASM357070v1_genomic.fna.gz --refList GCF_003570705.1_ASM357070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003570705.1_ASM357070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:17,628] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:17,647] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:17,648] [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_003570705.1	s__Bacillus_AZ zeae	100.0	1372	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_003937825.1	s__Mesobacillus subterraneus	77.9127	197	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166585.1	s__Mesobacillus jeotgali_A	77.7666	195	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613065.1	s__Neobacillus sp018613065	77.7597	125	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_018613315.1	s__Mesobacillus sp018613315	77.7437	176	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860125.1	s__Bacillus_BJ canaveralius	77.7315	98	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	99.48	99.12	0.94	0.92	4	-
GCF_018613055.1	s__Mesobacillus sp018613055	77.6832	196	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000813125.1	s__Mesobacillus selenatarsenatis	77.6723	184	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821085.1	s__Bacillus_D sp000821085	77.6628	111	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004340465.1	s__Bacillus_AZ foraminis	77.6436	213	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	97.82	96.47	0.93	0.88	4	-
GCF_018613155.1	s__Mesobacillus sp018613155	77.5623	182	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429105.1	s__Peribacillus glennii	77.5549	83	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656545.1	s__Neobacillus sp014656545	77.5319	99	1376	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_018424685.1	s__Mesobacillus boroniphilus_A	77.5013	195	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970675.1	s__Domibacillus tundrae	77.4538	54	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180615.1	s__Bacillus_BM vietnamensis_A	77.4497	52	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	98.11	98.11	0.91	0.91	2	-
GCF_000473245.1	s__Bacillus_AB infantis	77.2018	126	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AB	95.0	98.14	95.38	0.91	0.87	7	-
GCF_018343535.1	s__Neobacillus sp018343535	77.16	115	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCF_003316765.1	s__Bacillus_BM sp003316765	77.0774	73	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	98.55	98.55	0.89	0.89	2	-
GCF_003668575.1	s__Falsibacillus albus	77.0381	76	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000565285.1	s__Cytobacillus firmus_A	76.9909	139	1376	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_002272225.1	s__Cytobacillus sp002272225	76.9499	132	1376	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_001591465.1	s__Cytobacillus firmus	76.9301	131	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.21	98.02	0.95	0.85	11	-
GCF_003581585.1	s__Bacillus_BM salacetis	76.6989	74	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752035.1	s__Neobacillus rubiinfantis	76.5836	98	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:17,650] [INFO] GTDB search result was written to GCF_003570705.1_ASM357070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:17,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:17,657] [INFO] DFAST_QC result json was written to GCF_003570705.1_ASM357070v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:17,658] [INFO] DFAST_QC completed!
[2024-01-24 14:23:17,658] [INFO] Total running time: 0h1m27s