[2024-01-24 11:26:03,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:03,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:03,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c3ea71d-0e7d-4d34-aede-2f18752acce4/dqc_reference
[2024-01-24 11:26:04,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,147] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,147] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeb75b85-f10b-45b9-b17a-75a809130f57/GCF_000708755.2_ASM70875v2_genomic.fna.gz | prodigal -d GCF_000708755.2_ASM70875v2_genomic.fna/cds.fna -a GCF_000708755.2_ASM70875v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:13,989] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:13,989] [INFO] Task started: HMMsearch
[2024-01-24 11:26:13,990] [INFO] Running command: hmmsearch --tblout GCF_000708755.2_ASM70875v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c3ea71d-0e7d-4d34-aede-2f18752acce4/dqc_reference/reference_markers.hmm GCF_000708755.2_ASM70875v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:14,214] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:14,216] [INFO] Found 6/6 markers.
[2024-01-24 11:26:14,249] [INFO] Query marker FASTA was written to GCF_000708755.2_ASM70875v2_genomic.fna/markers.fasta
[2024-01-24 11:26:14,249] [INFO] Task started: Blastn
[2024-01-24 11:26:14,249] [INFO] Running command: blastn -query GCF_000708755.2_ASM70875v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3ea71d-0e7d-4d34-aede-2f18752acce4/dqc_reference/reference_markers.fasta -out GCF_000708755.2_ASM70875v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:14,818] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:14,821] [INFO] Selected 20 target genomes.
[2024-01-24 11:26:14,822] [INFO] Target genome list was writen to GCF_000708755.2_ASM70875v2_genomic.fna/target_genomes.txt
[2024-01-24 11:26:14,888] [INFO] Task started: fastANI
[2024-01-24 11:26:14,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb75b85-f10b-45b9-b17a-75a809130f57/GCF_000708755.2_ASM70875v2_genomic.fna.gz --refList GCF_000708755.2_ASM70875v2_genomic.fna/target_genomes.txt --output GCF_000708755.2_ASM70875v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:29,636] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:29,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c3ea71d-0e7d-4d34-aede-2f18752acce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:29,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c3ea71d-0e7d-4d34-aede-2f18752acce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:29,650] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:29,650] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:29,651] [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
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	100.0	1367	1369	95	conclusive
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	80.4703	720	1369	95	below_threshold
Metabacillus idriensis	strain=DSM 19097	GCA_009674765.1	324768	324768	type	True	80.4101	723	1369	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	80.1658	649	1369	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.8573	81	1369	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.498	133	1369	95	below_threshold
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	77.3579	100	1369	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	77.3307	54	1369	95	below_threshold
Mesobacillus subterraneus	strain=DSM 13966	GCA_003937825.1	285983	285983	suspected-type	True	77.3212	89	1369	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	77.2963	120	1369	95	below_threshold
Metabacillus lacus	strain=KCTC 33946	GCA_009674805.1	1983721	1983721	type	True	77.2885	134	1369	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.1323	77	1369	95	below_threshold
Metabacillus mangrovi	strain=KCTC 33872	GCA_009711125.1	1491830	1491830	type	True	77.1031	139	1369	95	below_threshold
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	77.0963	88	1369	95	below_threshold
Bacillus salacetis	strain=SKP7-4	GCA_003581585.1	2315464	2315464	type	True	76.9256	81	1369	95	below_threshold
Rossellomorea vietnamensis	strain=NBRC 101237	GCA_001591825.1	218284	218284	suspected-type	True	76.6363	75	1369	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	76.5593	73	1369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:29,652] [INFO] DFAST Taxonomy check result was written to GCF_000708755.2_ASM70875v2_genomic.fna/tc_result.tsv
[2024-01-24 11:26:29,652] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:29,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:29,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c3ea71d-0e7d-4d34-aede-2f18752acce4/dqc_reference/checkm_data
[2024-01-24 11:26:29,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:29,692] [INFO] Task started: CheckM
[2024-01-24 11:26:29,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000708755.2_ASM70875v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000708755.2_ASM70875v2_genomic.fna/checkm_input GCF_000708755.2_ASM70875v2_genomic.fna/checkm_result
[2024-01-24 11:27:03,296] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:03,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:03,315] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:03,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:03,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000708755.2_ASM70875v2_genomic.fna/markers.fasta)
[2024-01-24 11:27:03,315] [INFO] Task started: Blastn
[2024-01-24 11:27:03,315] [INFO] Running command: blastn -query GCF_000708755.2_ASM70875v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3ea71d-0e7d-4d34-aede-2f18752acce4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000708755.2_ASM70875v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:04,076] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:04,079] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:04,079] [INFO] Target genome list was writen to GCF_000708755.2_ASM70875v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:04,093] [INFO] Task started: fastANI
[2024-01-24 11:27:04,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb75b85-f10b-45b9-b17a-75a809130f57/GCF_000708755.2_ASM70875v2_genomic.fna.gz --refList GCF_000708755.2_ASM70875v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000708755.2_ASM70875v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:18,188] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:18,204] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:18,205] [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_000708755.2	s__Bacillus_P indicus	100.0	1367	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	97.93	97.85	0.93	0.91	3	conclusive
GCF_009674765.1	s__Bacillus_P idriensis	80.4017	724	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.40	95.01	0.92	0.87	5	-
GCF_014235785.1	s__Bacillus_P sp002858905	79.4083	469	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.85	98.20	0.93	0.90	4	-
GCF_001420595.1	s__Cytobacillus solani	77.8573	81	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_018283675.1	s__Metabacillus_B sp018283675	77.4571	133	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003816055.1	s__Metabacillus_B sp003816055	77.3454	151	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	77.3197	119	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_000732485.2	s__Metabacillus_B sp000732485	77.315	141	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674805.1	s__Metabacillus_C lacus	77.2885	134	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937825.1	s__Mesobacillus subterraneus	77.2315	92	1369	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_000518865.1	s__Metabacillus sp000518865	77.1289	112	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711125.1	s__Metabacillus_B mangrovi	77.1031	139	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813125.1	s__Mesobacillus selenatarsenatis	77.0987	88	1369	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_018613315.1	s__Mesobacillus sp018613315	77.083	88	1369	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_014837155.1	s__Litchfieldia sp014837155	77.034	68	1369	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_000294775.2	s__Cytobacillus oceanisediminis_B	76.9719	107	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_016908195.1	s__Jeotgalibacillus terrae	76.7948	57	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004124315.1	s__Bacillus cabrialesii	76.793	110	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_004405105.1	s__Jeotgalibacillus sp004405105	76.6227	63	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	76.4438	96	1369	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:18,206] [INFO] GTDB search result was written to GCF_000708755.2_ASM70875v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:18,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:18,211] [INFO] DFAST_QC result json was written to GCF_000708755.2_ASM70875v2_genomic.fna/dqc_result.json
[2024-01-24 11:27:18,211] [INFO] DFAST_QC completed!
[2024-01-24 11:27:18,211] [INFO] Total running time: 0h1m15s