[2024-01-24 14:14:05,850] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:05,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:05,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg078d13aa-bc2f-4266-905a-5a553b09df9f/dqc_reference
[2024-01-24 14:14:07,226] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,227] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,227] [INFO] Running command: gunzip -c /var/lib/cwl/stgedcd3ca4-979d-4e63-ba01-bcf9cd9018d2/GCF_009602435.1_ASM960243v1_genomic.fna.gz | prodigal -d GCF_009602435.1_ASM960243v1_genomic.fna/cds.fna -a GCF_009602435.1_ASM960243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:18,419] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:18,420] [INFO] Task started: HMMsearch
[2024-01-24 14:14:18,420] [INFO] Running command: hmmsearch --tblout GCF_009602435.1_ASM960243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg078d13aa-bc2f-4266-905a-5a553b09df9f/dqc_reference/reference_markers.hmm GCF_009602435.1_ASM960243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:18,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:18,812] [INFO] Found 6/6 markers.
[2024-01-24 14:14:18,851] [INFO] Query marker FASTA was written to GCF_009602435.1_ASM960243v1_genomic.fna/markers.fasta
[2024-01-24 14:14:18,851] [INFO] Task started: Blastn
[2024-01-24 14:14:18,851] [INFO] Running command: blastn -query GCF_009602435.1_ASM960243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg078d13aa-bc2f-4266-905a-5a553b09df9f/dqc_reference/reference_markers.fasta -out GCF_009602435.1_ASM960243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:19,565] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:19,569] [INFO] Selected 21 target genomes.
[2024-01-24 14:14:19,569] [INFO] Target genome list was writen to GCF_009602435.1_ASM960243v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:19,602] [INFO] Task started: fastANI
[2024-01-24 14:14:19,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgedcd3ca4-979d-4e63-ba01-bcf9cd9018d2/GCF_009602435.1_ASM960243v1_genomic.fna.gz --refList GCF_009602435.1_ASM960243v1_genomic.fna/target_genomes.txt --output GCF_009602435.1_ASM960243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:34,257] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:34,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg078d13aa-bc2f-4266-905a-5a553b09df9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:34,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg078d13aa-bc2f-4266-905a-5a553b09df9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:34,265] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:34,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:34,266] [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
Sediminibacillus terrae	strain=JSM 102062	GCA_009602435.1	1562106	1562106	type	True	100.0	1353	1353	95	conclusive
Sediminibacillus dalangtanensis	strain=DP4-553-S	GCA_017792025.1	2729421	2729421	type	True	87.567	1167	1353	95	below_threshold
Sediminibacillus halophilus	strain=CGMCC 1.6199	GCA_900103695.1	482461	482461	type	True	86.404	1145	1353	95	below_threshold
Sediminibacillus albus	strain=CGMCC 1.6502	GCA_900101125.1	407036	407036	type	True	78.5753	388	1353	95	below_threshold
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	78.2758	73	1353	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	77.5458	60	1353	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.8215	63	1353	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	76.7611	63	1353	95	below_threshold
Terribacillus halophilus	strain=DSM 21620	GCA_900101385.1	361279	361279	type	True	76.7205	62	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:34,267] [INFO] DFAST Taxonomy check result was written to GCF_009602435.1_ASM960243v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:34,268] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:34,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:34,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg078d13aa-bc2f-4266-905a-5a553b09df9f/dqc_reference/checkm_data
[2024-01-24 14:14:34,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:34,313] [INFO] Task started: CheckM
[2024-01-24 14:14:34,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009602435.1_ASM960243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009602435.1_ASM960243v1_genomic.fna/checkm_input GCF_009602435.1_ASM960243v1_genomic.fna/checkm_result
[2024-01-24 14:15:11,030] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:11,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:11,051] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:11,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:11,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009602435.1_ASM960243v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:11,052] [INFO] Task started: Blastn
[2024-01-24 14:15:11,052] [INFO] Running command: blastn -query GCF_009602435.1_ASM960243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg078d13aa-bc2f-4266-905a-5a553b09df9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009602435.1_ASM960243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:11,873] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:11,879] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:11,879] [INFO] Target genome list was writen to GCF_009602435.1_ASM960243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:11,888] [INFO] Task started: fastANI
[2024-01-24 14:15:11,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgedcd3ca4-979d-4e63-ba01-bcf9cd9018d2/GCF_009602435.1_ASM960243v1_genomic.fna.gz --refList GCF_009602435.1_ASM960243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009602435.1_ASM960243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:22,048] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:22,055] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:22,055] [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_009602435.1	s__Sediminibacillus terrae	100.0	1353	1353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	99.15	99.14	0.93	0.93	3	conclusive
GCF_017792025.1	s__Sediminibacillus sp017792025	87.5709	1166	1353	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_900103695.1	s__Sediminibacillus halophilus	86.3998	1146	1353	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_000821245.2	s__Sediminibacillus senegalensis	81.9343	818	1353	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_900101125.1	s__Sediminibacillus albus	78.5772	388	1353	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_900156915.1	s__Sediminibacillus_A massiliensis	77.5542	206	1353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.7847	64	1353	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_000770635.1	s__Pontibacillus yanchengensis	76.3806	54	1353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:22,057] [INFO] GTDB search result was written to GCF_009602435.1_ASM960243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:22,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:22,060] [INFO] DFAST_QC result json was written to GCF_009602435.1_ASM960243v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:22,060] [INFO] DFAST_QC completed!
[2024-01-24 14:15:22,061] [INFO] Total running time: 0h1m16s