[2024-01-24 11:51:37,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg54586ae3-9ed0-4962-acec-e080411e3035/dqc_reference
[2024-01-24 11:51:38,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,554] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,554] [INFO] Running command: gunzip -c /var/lib/cwl/stge45abc02-f0dc-45b9-92b2-c9af8f342743/GCF_017599325.1_ASM1759932v1_genomic.fna.gz | prodigal -d GCF_017599325.1_ASM1759932v1_genomic.fna/cds.fna -a GCF_017599325.1_ASM1759932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:43,706] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:43,706] [INFO] Task started: HMMsearch
[2024-01-24 11:51:43,706] [INFO] Running command: hmmsearch --tblout GCF_017599325.1_ASM1759932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54586ae3-9ed0-4962-acec-e080411e3035/dqc_reference/reference_markers.hmm GCF_017599325.1_ASM1759932v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:43,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:43,929] [INFO] Found 6/6 markers.
[2024-01-24 11:51:43,958] [INFO] Query marker FASTA was written to GCF_017599325.1_ASM1759932v1_genomic.fna/markers.fasta
[2024-01-24 11:51:43,958] [INFO] Task started: Blastn
[2024-01-24 11:51:43,959] [INFO] Running command: blastn -query GCF_017599325.1_ASM1759932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54586ae3-9ed0-4962-acec-e080411e3035/dqc_reference/reference_markers.fasta -out GCF_017599325.1_ASM1759932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:44,549] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:44,552] [INFO] Selected 28 target genomes.
[2024-01-24 11:51:44,552] [INFO] Target genome list was writen to GCF_017599325.1_ASM1759932v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:44,605] [INFO] Task started: fastANI
[2024-01-24 11:51:44,605] [INFO] Running command: fastANI --query /var/lib/cwl/stge45abc02-f0dc-45b9-92b2-c9af8f342743/GCF_017599325.1_ASM1759932v1_genomic.fna.gz --refList GCF_017599325.1_ASM1759932v1_genomic.fna/target_genomes.txt --output GCF_017599325.1_ASM1759932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:55,467] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:55,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54586ae3-9ed0-4962-acec-e080411e3035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:55,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54586ae3-9ed0-4962-acec-e080411e3035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:55,475] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:55,476] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:55,476] [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
Marinilactibacillus psychrotolerans	strain=DSM 19582	GCA_900101525.1	191770	191770	type	True	79.1179	235	846	95	below_threshold
Marinilactibacillus psychrotolerans	strain=M13-2T	GCA_019650195.1	191770	191770	type	True	79.0469	234	846	95	below_threshold
Marinilactibacillus psychrotolerans	strain=NBRC 100002	GCA_007989385.1	191770	191770	type	True	78.9948	231	846	95	below_threshold
Alkalibacterium putridalgicola	strain=NBRC 103243	GCA_007988845.1	426703	426703	type	True	78.0787	57	846	95	below_threshold
Alkalibacterium putridalgicola	strain=DSM 19182	GCA_900109825.1	426703	426703	type	True	77.9558	57	846	95	below_threshold
Alkalibacterium pelagium	strain=DSM 19183	GCA_900109325.1	426702	426702	type	True	77.6121	60	846	95	below_threshold
Alkalibacterium pelagium	strain=NBRC 103242	GCA_007991315.1	426702	426702	type	True	77.5881	60	846	95	below_threshold
Carnobacterium inhibens subsp. inhibens	strain=K1	GCA_000746825.1	1758721	147709	type	True	76.9103	61	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:55,479] [INFO] DFAST Taxonomy check result was written to GCF_017599325.1_ASM1759932v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:55,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:55,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:55,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54586ae3-9ed0-4962-acec-e080411e3035/dqc_reference/checkm_data
[2024-01-24 11:51:55,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:55,512] [INFO] Task started: CheckM
[2024-01-24 11:51:55,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017599325.1_ASM1759932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017599325.1_ASM1759932v1_genomic.fna/checkm_input GCF_017599325.1_ASM1759932v1_genomic.fna/checkm_result
[2024-01-24 11:52:18,095] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:18,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:18,116] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:18,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:18,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017599325.1_ASM1759932v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:18,117] [INFO] Task started: Blastn
[2024-01-24 11:52:18,117] [INFO] Running command: blastn -query GCF_017599325.1_ASM1759932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54586ae3-9ed0-4962-acec-e080411e3035/dqc_reference/reference_markers_gtdb.fasta -out GCF_017599325.1_ASM1759932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:18,912] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:18,916] [INFO] Selected 24 target genomes.
[2024-01-24 11:52:18,916] [INFO] Target genome list was writen to GCF_017599325.1_ASM1759932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:18,950] [INFO] Task started: fastANI
[2024-01-24 11:52:18,951] [INFO] Running command: fastANI --query /var/lib/cwl/stge45abc02-f0dc-45b9-92b2-c9af8f342743/GCF_017599325.1_ASM1759932v1_genomic.fna.gz --refList GCF_017599325.1_ASM1759932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017599325.1_ASM1759932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:29,393] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:29,406] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:29,406] [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_017599325.1	s__Marinilactibacillus sp017599325	100.0	841	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101525.1	s__Marinilactibacillus psychrotolerans	79.1471	236	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	98.27	97.67	0.87	0.82	5	-
GCF_900169305.1	s__Marinilactibacillus piezotolerans_A	78.91	192	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109825.1	s__Alkalibacterium putridalgicola	78.0055	55	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900109325.1	s__Alkalibacterium pelagium	77.6256	61	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003003275.1	s__Alkalibacterium olivapovliticus	77.4871	78	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746825.1	s__Carnobacterium_A inhibens	76.9103	61	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:29,408] [INFO] GTDB search result was written to GCF_017599325.1_ASM1759932v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:29,409] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:29,413] [INFO] DFAST_QC result json was written to GCF_017599325.1_ASM1759932v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:29,413] [INFO] DFAST_QC completed!
[2024-01-24 11:52:29,413] [INFO] Total running time: 0h0m52s