[2024-01-24 13:49:12,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:12,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:12,046] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb953335-9445-4076-94ce-17df7fe2dfeb/dqc_reference
[2024-01-24 13:49:13,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:13,360] [INFO] Task started: Prodigal
[2024-01-24 13:49:13,360] [INFO] Running command: gunzip -c /var/lib/cwl/stgf12090a2-720a-47bb-b78a-cbcd64857505/GCF_006007885.1_ASM600788v1_genomic.fna.gz | prodigal -d GCF_006007885.1_ASM600788v1_genomic.fna/cds.fna -a GCF_006007885.1_ASM600788v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:23,660] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:23,661] [INFO] Task started: HMMsearch
[2024-01-24 13:49:23,661] [INFO] Running command: hmmsearch --tblout GCF_006007885.1_ASM600788v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb953335-9445-4076-94ce-17df7fe2dfeb/dqc_reference/reference_markers.hmm GCF_006007885.1_ASM600788v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:23,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:23,942] [INFO] Found 6/6 markers.
[2024-01-24 13:49:23,981] [INFO] Query marker FASTA was written to GCF_006007885.1_ASM600788v1_genomic.fna/markers.fasta
[2024-01-24 13:49:23,981] [INFO] Task started: Blastn
[2024-01-24 13:49:23,982] [INFO] Running command: blastn -query GCF_006007885.1_ASM600788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb953335-9445-4076-94ce-17df7fe2dfeb/dqc_reference/reference_markers.fasta -out GCF_006007885.1_ASM600788v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:24,596] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:24,600] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:24,600] [INFO] Target genome list was writen to GCF_006007885.1_ASM600788v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:24,630] [INFO] Task started: fastANI
[2024-01-24 13:49:24,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12090a2-720a-47bb-b78a-cbcd64857505/GCF_006007885.1_ASM600788v1_genomic.fna.gz --refList GCF_006007885.1_ASM600788v1_genomic.fna/target_genomes.txt --output GCF_006007885.1_ASM600788v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:40,359] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:40,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb953335-9445-4076-94ce-17df7fe2dfeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:40,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb953335-9445-4076-94ce-17df7fe2dfeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:40,373] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:40,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:40,374] [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
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	100.0	1313	1313	95	conclusive
Alteribacter lacisalsi	strain=YSP-3	GCA_003226345.1	2045244	2045244	type	True	80.4696	668	1313	95	below_threshold
Alteribacter keqinensis	strain=KQ-3	GCA_003710255.1	2483800	2483800	type	True	78.0199	301	1313	95	below_threshold
Alteribacter salitolerans	strain=APA H-16(1)	GCA_016901055.1	2912333	2912333	type	True	78.0011	299	1313	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	77.9807	203	1313	95	below_threshold
Evansella caseinilytica	strain=SP	GCA_900107275.1	1503961	1503961	type	True	77.615	57	1313	95	below_threshold
Evansella clarkii	strain=DSM 8720	GCA_002019695.1	79879	79879	type	True	77.1844	84	1313	95	below_threshold
Alkalicoccus urumqiensis	strain=BZ-SZ-XJ18	GCA_002993335.1	1548213	1548213	type	True	76.9447	69	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:40,376] [INFO] DFAST Taxonomy check result was written to GCF_006007885.1_ASM600788v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:40,376] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:40,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:40,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb953335-9445-4076-94ce-17df7fe2dfeb/dqc_reference/checkm_data
[2024-01-24 13:49:40,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:40,420] [INFO] Task started: CheckM
[2024-01-24 13:49:40,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006007885.1_ASM600788v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006007885.1_ASM600788v1_genomic.fna/checkm_input GCF_006007885.1_ASM600788v1_genomic.fna/checkm_result
[2024-01-24 13:50:16,620] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:16,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:16,666] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:16,667] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:16,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006007885.1_ASM600788v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:16,667] [INFO] Task started: Blastn
[2024-01-24 13:50:16,667] [INFO] Running command: blastn -query GCF_006007885.1_ASM600788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb953335-9445-4076-94ce-17df7fe2dfeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_006007885.1_ASM600788v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:17,471] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:17,475] [INFO] Selected 23 target genomes.
[2024-01-24 13:50:17,475] [INFO] Target genome list was writen to GCF_006007885.1_ASM600788v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:17,701] [INFO] Task started: fastANI
[2024-01-24 13:50:17,702] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12090a2-720a-47bb-b78a-cbcd64857505/GCF_006007885.1_ASM600788v1_genomic.fna.gz --refList GCF_006007885.1_ASM600788v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006007885.1_ASM600788v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:35,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:35,609] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:35,609] [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_006007885.1	s__Alteribacter natronophilus	100.0	1313	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003226345.1	s__Alteribacter lacisalsi	80.4762	665	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710255.1	s__Alteribacter sp003710255	78.0199	301	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	98.04	98.04	0.95	0.95	2	-
GCF_000429705.1	s__Alteribacter aurantiacus	77.9987	202	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002352765.1	s__Alteribacter populi	77.995	145	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	99.66	99.66	0.95	0.95	2	-
GCF_002019695.1	s__Evansella clarkii	77.1813	85	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	98.30	98.30	0.93	0.93	2	-
GCF_002993335.1	s__Alkalicoccus urumqiensis	76.9447	69	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:35,611] [INFO] GTDB search result was written to GCF_006007885.1_ASM600788v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:35,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:35,616] [INFO] DFAST_QC result json was written to GCF_006007885.1_ASM600788v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:35,616] [INFO] DFAST_QC completed!
[2024-01-24 13:50:35,616] [INFO] Total running time: 0h1m24s