[2024-01-24 13:36:31,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d879eac-8ec3-44c1-a0ae-692fcb55c496/dqc_reference
[2024-01-24 13:36:33,192] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,193] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,193] [INFO] Running command: gunzip -c /var/lib/cwl/stg81e37b66-04a1-48e5-8157-1b414815a241/GCF_021166585.1_ASM2116658v1_genomic.fna.gz | prodigal -d GCF_021166585.1_ASM2116658v1_genomic.fna/cds.fna -a GCF_021166585.1_ASM2116658v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:43,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:43,450] [INFO] Task started: HMMsearch
[2024-01-24 13:36:43,450] [INFO] Running command: hmmsearch --tblout GCF_021166585.1_ASM2116658v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d879eac-8ec3-44c1-a0ae-692fcb55c496/dqc_reference/reference_markers.hmm GCF_021166585.1_ASM2116658v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:43,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:43,737] [INFO] Found 6/6 markers.
[2024-01-24 13:36:43,774] [INFO] Query marker FASTA was written to GCF_021166585.1_ASM2116658v1_genomic.fna/markers.fasta
[2024-01-24 13:36:43,775] [INFO] Task started: Blastn
[2024-01-24 13:36:43,775] [INFO] Running command: blastn -query GCF_021166585.1_ASM2116658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d879eac-8ec3-44c1-a0ae-692fcb55c496/dqc_reference/reference_markers.fasta -out GCF_021166585.1_ASM2116658v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:44,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:44,394] [INFO] Selected 28 target genomes.
[2024-01-24 13:36:44,395] [INFO] Target genome list was writen to GCF_021166585.1_ASM2116658v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:44,408] [INFO] Task started: fastANI
[2024-01-24 13:36:44,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e37b66-04a1-48e5-8157-1b414815a241/GCF_021166585.1_ASM2116658v1_genomic.fna.gz --refList GCF_021166585.1_ASM2116658v1_genomic.fna/target_genomes.txt --output GCF_021166585.1_ASM2116658v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:02,531] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:02,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d879eac-8ec3-44c1-a0ae-692fcb55c496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:02,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d879eac-8ec3-44c1-a0ae-692fcb55c496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:02,546] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:02,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:02,547] [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 kandeliae	strain=GX 13764	GCA_021166585.1	2900151	2900151	type	True	100.0	1394	1394	95	conclusive
Metabacillus lacus	strain=KCTC 33946	GCA_009674805.1	1983721	1983721	type	True	77.1209	126	1394	95	below_threshold
Metabacillus mangrovi	strain=KCTC 33872	GCA_009711125.1	1491830	1491830	type	True	77.1047	174	1394	95	below_threshold
Bacillus velezensis	strain=KCTC 13012	GCA_001267695.1	492670	492670	type	True	76.9391	78	1394	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	76.9156	138	1394	95	below_threshold
Bacillus velezensis	strain=NRRL B-41580	GCA_001461825.1	492670	492670	type	True	76.8782	77	1394	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	76.8549	73	1394	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_013618945.1	1917180	1917180	type	True	76.8245	73	1394	95	below_threshold
Bacillus atrophaeus	strain=NRRL NRS 213	GCA_001584335.1	1452	1452	type	True	76.709	90	1394	95	below_threshold
Bacillus atrophaeus	strain=NBRC 15539	GCA_001591925.1	1452	1452	type	True	76.6729	92	1394	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	76.5944	50	1394	95	below_threshold
Mesobacillus subterraneus	strain=DSM 13966	GCA_003937825.1	285983	285983	suspected-type	True	76.577	80	1394	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	76.5257	95	1394	95	below_threshold
Bacillus swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	76.4973	94	1394	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.3913	68	1394	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.3558	91	1394	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	76.3458	67	1394	95	below_threshold
Bacillus marinisedimentorum	strain=NC2-31	GCA_001644195.2	1821260	1821260	type	True	76.1779	59	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:02,549] [INFO] DFAST Taxonomy check result was written to GCF_021166585.1_ASM2116658v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:02,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:02,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:02,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d879eac-8ec3-44c1-a0ae-692fcb55c496/dqc_reference/checkm_data
[2024-01-24 13:37:02,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:02,593] [INFO] Task started: CheckM
[2024-01-24 13:37:02,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021166585.1_ASM2116658v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021166585.1_ASM2116658v1_genomic.fna/checkm_input GCF_021166585.1_ASM2116658v1_genomic.fna/checkm_result
[2024-01-24 13:37:39,623] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:39,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,642] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:39,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:39,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021166585.1_ASM2116658v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:39,642] [INFO] Task started: Blastn
[2024-01-24 13:37:39,643] [INFO] Running command: blastn -query GCF_021166585.1_ASM2116658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d879eac-8ec3-44c1-a0ae-692fcb55c496/dqc_reference/reference_markers_gtdb.fasta -out GCF_021166585.1_ASM2116658v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:40,546] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:40,550] [INFO] Selected 29 target genomes.
[2024-01-24 13:37:40,551] [INFO] Target genome list was writen to GCF_021166585.1_ASM2116658v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:40,580] [INFO] Task started: fastANI
[2024-01-24 13:37:40,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e37b66-04a1-48e5-8157-1b414815a241/GCF_021166585.1_ASM2116658v1_genomic.fna.gz --refList GCF_021166585.1_ASM2116658v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021166585.1_ASM2116658v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:58,922] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:58,938] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:37:58,939] [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_000732485.2	s__Metabacillus_B sp000732485	77.3733	190	1394	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	77.2704	180	1394	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	77.1209	126	1394	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_009711125.1	s__Metabacillus_B mangrovi	77.0891	175	1394	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_001461825.1	s__Bacillus velezensis	76.9423	75	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.12	97.33	0.94	0.90	498	-
GCF_010093085.1	s__Bacillus sp010093085	76.9075	77	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969855.1	s__Bacillus haynesii	76.9015	82	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_003570705.1	s__Bacillus_AZ zeae	76.8565	72	1394	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	-
GCF_001042475.2	s__Bacillus glycinifermentans	76.7285	85	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.06	95.94	0.90	0.86	8	-
GCF_001278705.1	s__Bacillus gobiensis	76.688	63	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.94	99.94	0.99	0.99	2	-
GCF_001026695.1	s__Neobacillus vireti	76.6385	76	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003937825.1	s__Mesobacillus subterraneus	76.5749	79	1394	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_002863585.1	s__Bacillus_AI deserti_A	76.5722	70	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860165.1	s__Bacillus_BJ sp002860165	76.5511	64	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969815.1	s__Bacillus swezeyi	76.4739	93	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_003429105.1	s__Peribacillus glennii	76.4585	59	1394	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_000300535.1	s__Bacillus xiamenensis	76.4502	69	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.27	99.24	0.95	0.94	4	-
GCF_001274725.1	s__Cytobacillus globisporus	76.4366	89	1394	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_017303275.1	s__Cytobacillus sp017303275	76.4134	87	1394	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_001636315.1	s__Neobacillus mesonae	76.3458	67	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,940] [INFO] GTDB search result was written to GCF_021166585.1_ASM2116658v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:58,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:58,944] [INFO] DFAST_QC result json was written to GCF_021166585.1_ASM2116658v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:58,945] [INFO] DFAST_QC completed!
[2024-01-24 13:37:58,945] [INFO] Total running time: 0h1m27s