[2024-01-25 18:06:20,404] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg794667fe-2625-45f4-8a96-acfa9d4cefb2/dqc_reference
[2024-01-25 18:06:21,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:21,540] [INFO] Task started: Prodigal
[2024-01-25 18:06:21,540] [INFO] Running command: gunzip -c /var/lib/cwl/stge1d9774a-5eec-4a94-887d-d75176957cad/GCF_030067815.1_ASM3006781v1_genomic.fna.gz | prodigal -d GCF_030067815.1_ASM3006781v1_genomic.fna/cds.fna -a GCF_030067815.1_ASM3006781v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:29,666] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:29,666] [INFO] Task started: HMMsearch
[2024-01-25 18:06:29,666] [INFO] Running command: hmmsearch --tblout GCF_030067815.1_ASM3006781v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg794667fe-2625-45f4-8a96-acfa9d4cefb2/dqc_reference/reference_markers.hmm GCF_030067815.1_ASM3006781v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:29,902] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:29,903] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge1d9774a-5eec-4a94-887d-d75176957cad/GCF_030067815.1_ASM3006781v1_genomic.fna.gz]
[2024-01-25 18:06:29,933] [INFO] Query marker FASTA was written to GCF_030067815.1_ASM3006781v1_genomic.fna/markers.fasta
[2024-01-25 18:06:29,933] [INFO] Task started: Blastn
[2024-01-25 18:06:29,933] [INFO] Running command: blastn -query GCF_030067815.1_ASM3006781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg794667fe-2625-45f4-8a96-acfa9d4cefb2/dqc_reference/reference_markers.fasta -out GCF_030067815.1_ASM3006781v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:30,481] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:30,484] [INFO] Selected 35 target genomes.
[2024-01-25 18:06:30,484] [INFO] Target genome list was writen to GCF_030067815.1_ASM3006781v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:30,513] [INFO] Task started: fastANI
[2024-01-25 18:06:30,513] [INFO] Running command: fastANI --query /var/lib/cwl/stge1d9774a-5eec-4a94-887d-d75176957cad/GCF_030067815.1_ASM3006781v1_genomic.fna.gz --refList GCF_030067815.1_ASM3006781v1_genomic.fna/target_genomes.txt --output GCF_030067815.1_ASM3006781v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:51,878] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:51,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg794667fe-2625-45f4-8a96-acfa9d4cefb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:51,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg794667fe-2625-45f4-8a96-acfa9d4cefb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:51,885] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:06:51,885] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:06:51,885] [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
Sporosarcina luteola	strain=NBRC 105378	GCA_007991495.1	582850	582850	type	True	80.7258	579	1219	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	80.6132	52	1219	95	below_threshold
Sporosarcina limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	78.2566	153	1219	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	77.6679	169	1219	95	below_threshold
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	77.1366	72	1219	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	77.0791	71	1219	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	76.7661	51	1219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:51,887] [INFO] DFAST Taxonomy check result was written to GCF_030067815.1_ASM3006781v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:51,888] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:51,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:51,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg794667fe-2625-45f4-8a96-acfa9d4cefb2/dqc_reference/checkm_data
[2024-01-25 18:06:51,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:51,932] [INFO] Task started: CheckM
[2024-01-25 18:06:51,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030067815.1_ASM3006781v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030067815.1_ASM3006781v1_genomic.fna/checkm_input GCF_030067815.1_ASM3006781v1_genomic.fna/checkm_result
[2024-01-25 18:07:19,844] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:19,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:19,874] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:19,874] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:19,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030067815.1_ASM3006781v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:19,875] [INFO] Task started: Blastn
[2024-01-25 18:07:19,875] [INFO] Running command: blastn -query GCF_030067815.1_ASM3006781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg794667fe-2625-45f4-8a96-acfa9d4cefb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_030067815.1_ASM3006781v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:20,748] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:20,751] [INFO] Selected 37 target genomes.
[2024-01-25 18:07:20,751] [INFO] Target genome list was writen to GCF_030067815.1_ASM3006781v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:20,789] [INFO] Task started: fastANI
[2024-01-25 18:07:20,789] [INFO] Running command: fastANI --query /var/lib/cwl/stge1d9774a-5eec-4a94-887d-d75176957cad/GCF_030067815.1_ASM3006781v1_genomic.fna.gz --refList GCF_030067815.1_ASM3006781v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030067815.1_ASM3006781v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:47,156] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:47,167] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:07:47,168] [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_007991495.1	s__Sporosarcina luteola	80.7319	577	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001531445.1	s__Sporosarcina koreensis_C	79.9448	534	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004367585.1	s__Paenisporosarcina antarctica	79.689	63	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	95.47	95.47	0.86	0.86	2	-
GCF_018140925.1	s__Psychrobacillus sp018140925	79.5853	89	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077155.1	s__Sporosarcina sp002077155	79.5695	99	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.91	98.90	0.90	0.90	3	-
GCF_017498505.1	s__Sporosarcina sp017498505	78.7456	233	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590685.1	s__Sporosarcina psychrophila	78.6241	189	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.26	98.26	0.89	0.89	2	-
GCF_000829195.1	s__Sporosarcina sp000829195	78.4149	161	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204635.1	s__Sporosarcina luteola_A	78.2624	202	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873855.1	s__Sporosarcina limicola	78.2347	154	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369195.1	s__Sporosarcina sp008369195	77.7505	162	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820585.1	s__Sporosarcina sp016820585	77.7223	188	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408665.1	s__Sporosarcina sp013408665	77.6959	162	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609045.1	s__Sporosarcina tadaridae	77.6828	169	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017347095.1	s__Sporosarcina sp017347095	77.6322	173	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009651005.1	s__Sporosarcina sp009651005	77.5943	108	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282005.1	s__Sporosarcina sp014282005	77.5726	184	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	96.23	96.23	0.81	0.81	2	-
GCF_009650995.1	s__Sporosarcina sp009650995	77.5268	91	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103605.1	s__Psychrobacillus sp900103605	77.4729	83	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843435.1	s__Psychrobacillus sp012843435	76.5717	62	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:47,169] [INFO] GTDB search result was written to GCF_030067815.1_ASM3006781v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:47,169] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:47,172] [INFO] DFAST_QC result json was written to GCF_030067815.1_ASM3006781v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:47,172] [INFO] DFAST_QC completed!
[2024-01-25 18:07:47,172] [INFO] Total running time: 0h1m27s