[2024-01-24 15:27:08,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:08,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:08,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a5a1236-9745-44b4-a015-18a8b346fc58/dqc_reference
[2024-01-24 15:27:10,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:10,013] [INFO] Task started: Prodigal
[2024-01-24 15:27:10,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg816a8d0d-28a5-4c6d-9f3e-bd832fdca646/GCF_003369565.1_ASM336956v1_genomic.fna.gz | prodigal -d GCF_003369565.1_ASM336956v1_genomic.fna/cds.fna -a GCF_003369565.1_ASM336956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:17,995] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:17,995] [INFO] Task started: HMMsearch
[2024-01-24 15:27:17,995] [INFO] Running command: hmmsearch --tblout GCF_003369565.1_ASM336956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a5a1236-9745-44b4-a015-18a8b346fc58/dqc_reference/reference_markers.hmm GCF_003369565.1_ASM336956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:18,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:18,341] [INFO] Found 6/6 markers.
[2024-01-24 15:27:18,376] [INFO] Query marker FASTA was written to GCF_003369565.1_ASM336956v1_genomic.fna/markers.fasta
[2024-01-24 15:27:18,377] [INFO] Task started: Blastn
[2024-01-24 15:27:18,377] [INFO] Running command: blastn -query GCF_003369565.1_ASM336956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a5a1236-9745-44b4-a015-18a8b346fc58/dqc_reference/reference_markers.fasta -out GCF_003369565.1_ASM336956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:19,097] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:19,101] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:19,101] [INFO] Target genome list was writen to GCF_003369565.1_ASM336956v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:19,176] [INFO] Task started: fastANI
[2024-01-24 15:27:19,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg816a8d0d-28a5-4c6d-9f3e-bd832fdca646/GCF_003369565.1_ASM336956v1_genomic.fna.gz --refList GCF_003369565.1_ASM336956v1_genomic.fna/target_genomes.txt --output GCF_003369565.1_ASM336956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:33,792] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:33,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a5a1236-9745-44b4-a015-18a8b346fc58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:33,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a5a1236-9745-44b4-a015-18a8b346fc58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:33,811] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:33,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:33,811] [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
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	100.0	1319	1322	95	conclusive
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	87.0306	1044	1322	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	83.5742	879	1322	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	77.6938	165	1322	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	77.6619	234	1322	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	77.6423	235	1322	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.355	223	1322	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.1663	192	1322	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	76.9334	191	1322	95	below_threshold
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	76.8045	167	1322	95	below_threshold
Salirhabdus euzebyi	strain=DSM 19612	GCA_014207435.1	394506	394506	type	True	76.7318	53	1322	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.6887	62	1322	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.6092	120	1322	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.4639	120	1322	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	76.0949	50	1322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:33,813] [INFO] DFAST Taxonomy check result was written to GCF_003369565.1_ASM336956v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:33,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:33,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:33,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a5a1236-9745-44b4-a015-18a8b346fc58/dqc_reference/checkm_data
[2024-01-24 15:27:33,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:33,905] [INFO] Task started: CheckM
[2024-01-24 15:27:33,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003369565.1_ASM336956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003369565.1_ASM336956v1_genomic.fna/checkm_input GCF_003369565.1_ASM336956v1_genomic.fna/checkm_result
[2024-01-24 15:28:04,827] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:04,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:04,849] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:04,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:04,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003369565.1_ASM336956v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:04,851] [INFO] Task started: Blastn
[2024-01-24 15:28:04,851] [INFO] Running command: blastn -query GCF_003369565.1_ASM336956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a5a1236-9745-44b4-a015-18a8b346fc58/dqc_reference/reference_markers_gtdb.fasta -out GCF_003369565.1_ASM336956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:05,741] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:05,745] [INFO] Selected 18 target genomes.
[2024-01-24 15:28:05,746] [INFO] Target genome list was writen to GCF_003369565.1_ASM336956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:05,759] [INFO] Task started: fastANI
[2024-01-24 15:28:05,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg816a8d0d-28a5-4c6d-9f3e-bd832fdca646/GCF_003369565.1_ASM336956v1_genomic.fna.gz --refList GCF_003369565.1_ASM336956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003369565.1_ASM336956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:19,651] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:19,665] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:19,665] [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_003369565.1	s__Oceanobacillus chungangensis	100.0	1319	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003352005.1	s__Oceanobacillus zhaokaii	87.0328	1044	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_003369575.1	s__Oceanobacillus arenosus	83.5705	879	1322	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_009728145.1	s__Ornithinibacillus caprae	77.8421	145	1322	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_003515705.1	s__Oceanobacillus profundus	77.6944	234	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_001618145.1	s__Oceanobacillus damuensis	77.6788	165	1322	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_003628445.1	s__Oceanobacillus bengalensis	77.3697	221	1322	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_002266285.1	s__Virgibacillus_G indicus	77.3671	177	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224365.1	s__Virgibacillus_F necropolis	77.1947	117	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733865.1	s__Oceanobacillus salinisoli	77.1798	191	1322	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_000190475.1	s__Ornithinibacillus scapharcae	77.1748	123	1322	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_014905415.1	s__Virgibacillus salexigens	76.7843	134	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_017874115.1	s__Virgibacillus_H natechei	76.7703	166	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207435.1	s__Salirhabdus euzebyi	76.742	53	1322	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_009389585.1	s__Oceanobacillus sp009389585	76.6782	109	1322	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_900110695.1	s__Lentibacillus subterraneus	76.446	121	1322	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_003176895.1	s__Gracilibacillus dipsosauri	76.267	76	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:19,667] [INFO] GTDB search result was written to GCF_003369565.1_ASM336956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:19,668] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:19,672] [INFO] DFAST_QC result json was written to GCF_003369565.1_ASM336956v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:19,672] [INFO] DFAST_QC completed!
[2024-01-24 15:28:19,672] [INFO] Total running time: 0h1m11s