[2024-01-24 12:45:10,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg04cebb10-c614-4eb8-9ccd-118f540aa3ee/dqc_reference
[2024-01-24 12:45:13,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,087] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,087] [INFO] Running command: gunzip -c /var/lib/cwl/stga951bf2e-b20f-49ea-a5b1-0c26ef17bff7/GCF_020404745.1_ASM2040474v1_genomic.fna.gz | prodigal -d GCF_020404745.1_ASM2040474v1_genomic.fna/cds.fna -a GCF_020404745.1_ASM2040474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:21,002] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:21,003] [INFO] Task started: HMMsearch
[2024-01-24 12:45:21,003] [INFO] Running command: hmmsearch --tblout GCF_020404745.1_ASM2040474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04cebb10-c614-4eb8-9ccd-118f540aa3ee/dqc_reference/reference_markers.hmm GCF_020404745.1_ASM2040474v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:21,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:21,287] [INFO] Found 6/6 markers.
[2024-01-24 12:45:21,322] [INFO] Query marker FASTA was written to GCF_020404745.1_ASM2040474v1_genomic.fna/markers.fasta
[2024-01-24 12:45:21,323] [INFO] Task started: Blastn
[2024-01-24 12:45:21,323] [INFO] Running command: blastn -query GCF_020404745.1_ASM2040474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cebb10-c614-4eb8-9ccd-118f540aa3ee/dqc_reference/reference_markers.fasta -out GCF_020404745.1_ASM2040474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:21,919] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:21,923] [INFO] Selected 26 target genomes.
[2024-01-24 12:45:21,923] [INFO] Target genome list was writen to GCF_020404745.1_ASM2040474v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:22,003] [INFO] Task started: fastANI
[2024-01-24 12:45:22,004] [INFO] Running command: fastANI --query /var/lib/cwl/stga951bf2e-b20f-49ea-a5b1-0c26ef17bff7/GCF_020404745.1_ASM2040474v1_genomic.fna.gz --refList GCF_020404745.1_ASM2040474v1_genomic.fna/target_genomes.txt --output GCF_020404745.1_ASM2040474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:38,101] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:38,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04cebb10-c614-4eb8-9ccd-118f540aa3ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:38,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04cebb10-c614-4eb8-9ccd-118f540aa3ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:38,118] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:38,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:38,118] [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
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	100.0	1386	1386	95	conclusive
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	79.639	585	1386	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.9004	220	1386	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	77.7227	141	1386	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.7141	141	1386	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.702	178	1386	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.4192	225	1386	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.3087	109	1386	95	below_threshold
Sediminibacillus albus	strain=CGMCC 1.6502	GCA_900101125.1	407036	407036	type	True	77.27	126	1386	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.2513	167	1386	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.9953	106	1386	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.9731	70	1386	95	below_threshold
Halobacillus karajensis	strain=DSM 14948	GCA_900108515.1	195088	195088	type	True	76.9089	53	1386	95	below_threshold
Thalassobacillus cyri	strain=CCM7597	GCA_900107755.1	571932	571932	type	True	76.898	56	1386	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	76.8385	65	1386	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	76.8023	67	1386	95	below_threshold
Pontibacillus marinus	strain=DSM 16465	GCA_000425225.1	273164	273164	type	True	76.6524	60	1386	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	76.5607	102	1386	95	below_threshold
Pontibacillus marinus	strain=BH030004	GCA_000775605.1	273164	273164	type	True	76.4204	59	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:38,120] [INFO] DFAST Taxonomy check result was written to GCF_020404745.1_ASM2040474v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:38,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:38,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:38,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04cebb10-c614-4eb8-9ccd-118f540aa3ee/dqc_reference/checkm_data
[2024-01-24 12:45:38,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:38,168] [INFO] Task started: CheckM
[2024-01-24 12:45:38,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020404745.1_ASM2040474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020404745.1_ASM2040474v1_genomic.fna/checkm_input GCF_020404745.1_ASM2040474v1_genomic.fna/checkm_result
[2024-01-24 12:46:07,142] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:07,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:07,165] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:07,165] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:07,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020404745.1_ASM2040474v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:07,166] [INFO] Task started: Blastn
[2024-01-24 12:46:07,166] [INFO] Running command: blastn -query GCF_020404745.1_ASM2040474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cebb10-c614-4eb8-9ccd-118f540aa3ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_020404745.1_ASM2040474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:07,948] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:07,953] [INFO] Selected 34 target genomes.
[2024-01-24 12:46:07,953] [INFO] Target genome list was writen to GCF_020404745.1_ASM2040474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:08,709] [INFO] Task started: fastANI
[2024-01-24 12:46:08,710] [INFO] Running command: fastANI --query /var/lib/cwl/stga951bf2e-b20f-49ea-a5b1-0c26ef17bff7/GCF_020404745.1_ASM2040474v1_genomic.fna.gz --refList GCF_020404745.1_ASM2040474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020404745.1_ASM2040474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:30,104] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:30,137] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:30,138] [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_009649745.1	s__Aquibacillus_A halophilus	79.645	586	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	77.662	181	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	77.6352	140	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000821245.2	s__Sediminibacillus senegalensis	77.6148	89	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	77.472	225	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007301515.1	s__Radiobacillus deserti	77.4462	126	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.3939	122	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306965.1	s__Amphibacillus_C jilinensis	77.3456	59	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101125.1	s__Sediminibacillus albus	77.27	126	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.2605	110	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	77.2563	167	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_018075365.1	s__Virgibacillus pantothenticus	77.0784	75	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.9734	107	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_900107755.1	s__Thalassobacillus cyri	76.9418	55	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733865.1	s__Oceanobacillus salinisoli	76.9406	74	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108515.1	s__Halobacillus karajensis	76.9381	54	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.38	99.37	0.93	0.93	4	-
GCF_016908155.1	s__Oceanobacillus caeni	76.8984	71	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_014638995.1	s__Virgibacillus_E oceani	76.8792	75	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908375.1	s__Amphibacillus_C cookii	76.8703	73	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207435.1	s__Salirhabdus euzebyi	76.8244	76	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014636475.1	s__Halobacillus_A andaensis	76.7357	69	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240405.1	s__OEQK01 sp900240405	76.702	59	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__OEQK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425225.1	s__Pontibacillus marinus	76.6165	61	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009858175.1	s__Pontibacillus sp009858175	76.6048	63	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129485.1	s__Ornithinibacillus halophilus	76.4949	102	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002276165.1	s__Cytobacillus kochii	76.4421	53	1386	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_018918075.1	s__MSJ-26 sp018918075	76.2412	59	1386	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__MSJ-26	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:30,140] [INFO] GTDB search result was written to GCF_020404745.1_ASM2040474v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:30,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:30,146] [INFO] DFAST_QC result json was written to GCF_020404745.1_ASM2040474v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:30,146] [INFO] DFAST_QC completed!
[2024-01-24 12:46:30,146] [INFO] Total running time: 0h1m20s