[2024-01-25 19:45:50,592] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:50,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:50,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg95d54b53-c2dc-4cb8-85ac-c46d39979299/dqc_reference
[2024-01-25 19:45:51,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:51,721] [INFO] Task started: Prodigal
[2024-01-25 19:45:51,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a23ac15-417c-4beb-8c10-fd4d859674d8/GCF_016908555.1_ASM1690855v1_genomic.fna.gz | prodigal -d GCF_016908555.1_ASM1690855v1_genomic.fna/cds.fna -a GCF_016908555.1_ASM1690855v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:56,704] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:56,704] [INFO] Task started: HMMsearch
[2024-01-25 19:45:56,704] [INFO] Running command: hmmsearch --tblout GCF_016908555.1_ASM1690855v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95d54b53-c2dc-4cb8-85ac-c46d39979299/dqc_reference/reference_markers.hmm GCF_016908555.1_ASM1690855v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:56,929] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:56,930] [INFO] Found 6/6 markers.
[2024-01-25 19:45:56,956] [INFO] Query marker FASTA was written to GCF_016908555.1_ASM1690855v1_genomic.fna/markers.fasta
[2024-01-25 19:45:56,956] [INFO] Task started: Blastn
[2024-01-25 19:45:56,957] [INFO] Running command: blastn -query GCF_016908555.1_ASM1690855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95d54b53-c2dc-4cb8-85ac-c46d39979299/dqc_reference/reference_markers.fasta -out GCF_016908555.1_ASM1690855v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:57,530] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:57,532] [INFO] Selected 22 target genomes.
[2024-01-25 19:45:57,532] [INFO] Target genome list was writen to GCF_016908555.1_ASM1690855v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:57,560] [INFO] Task started: fastANI
[2024-01-25 19:45:57,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a23ac15-417c-4beb-8c10-fd4d859674d8/GCF_016908555.1_ASM1690855v1_genomic.fna.gz --refList GCF_016908555.1_ASM1690855v1_genomic.fna/target_genomes.txt --output GCF_016908555.1_ASM1690855v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:10,742] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:10,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95d54b53-c2dc-4cb8-85ac-c46d39979299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:10,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95d54b53-c2dc-4cb8-85ac-c46d39979299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:10,749] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:10,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:10,749] [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
Alkaliphilus hydrothermalis	strain=DSM 25890	GCA_016908555.1	1482730	1482730	type	True	100.0	996	998	95	conclusive
Alkaliphilus transvaalensis	strain=ATCC 700919	GCA_000621485.1	114628	114628	type	True	78.2122	239	998	95	below_threshold
Alkaliphilus serpentinus	strain=LacT	GCA_009017255.1	1482731	1482731	type	True	77.4806	96	998	95	below_threshold
Natronincola ferrireducens	strain=DSM 18346	GCA_900100845.1	393762	393762	type	True	77.0234	58	998	95	below_threshold
Natronincola peptidivorans	strain=DSM 18979	GCA_900111615.1	426128	426128	type	True	76.5258	64	998	95	below_threshold
Clostridium formicaceticum	strain=ATCC 27076	GCA_001854185.1	1497	1497	type	True	76.5135	82	998	95	below_threshold
Alkaliphilus peptidifermentans	strain=DSM 18978	GCA_900101495.1	426129	426129	type	True	76.5115	85	998	95	below_threshold
Clostridium formicaceticum	strain=DSM 92	GCA_002080475.1	1497	1497	type	True	76.5041	77	998	95	below_threshold
Anaerovirgula multivorans	strain=SCA	GCA_900188145.1	312168	312168	type	True	76.3551	84	998	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	76.2412	52	998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:10,751] [INFO] DFAST Taxonomy check result was written to GCF_016908555.1_ASM1690855v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:10,751] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:10,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:10,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95d54b53-c2dc-4cb8-85ac-c46d39979299/dqc_reference/checkm_data
[2024-01-25 19:46:10,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:10,786] [INFO] Task started: CheckM
[2024-01-25 19:46:10,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908555.1_ASM1690855v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908555.1_ASM1690855v1_genomic.fna/checkm_input GCF_016908555.1_ASM1690855v1_genomic.fna/checkm_result
[2024-01-25 19:46:30,933] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:30,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:30,954] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:30,954] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:30,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908555.1_ASM1690855v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:30,955] [INFO] Task started: Blastn
[2024-01-25 19:46:30,955] [INFO] Running command: blastn -query GCF_016908555.1_ASM1690855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95d54b53-c2dc-4cb8-85ac-c46d39979299/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908555.1_ASM1690855v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:31,889] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:31,898] [INFO] Selected 26 target genomes.
[2024-01-25 19:46:31,898] [INFO] Target genome list was writen to GCF_016908555.1_ASM1690855v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:31,932] [INFO] Task started: fastANI
[2024-01-25 19:46:31,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a23ac15-417c-4beb-8c10-fd4d859674d8/GCF_016908555.1_ASM1690855v1_genomic.fna.gz --refList GCF_016908555.1_ASM1690855v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908555.1_ASM1690855v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:46,357] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:46,368] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:46,368] [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_016908555.1	s__Alkaliphilus hydrothermalis	100.0	996	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000621485.1	s__Alkaliphilus transvaalensis	78.1975	240	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009017255.1	s__LacT sp009017255	77.4806	96	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__LacT	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100845.1	s__Natronincola ferrireducens	77.0234	58	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Natronincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141405.1	s__Serpentinicella alkaliphila	76.7768	66	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Serpentinicella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001854185.1	s__Clostridium_W formicaceticum	76.6503	83	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Clostridium_W	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111615.1	s__Natronincola_A peptidivorans	76.5258	64	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Natronincola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101495.1	s__Alkaliphilus_C peptidifermentans	76.5115	85	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188145.1	s__Anaerovirgula multivorans	76.3551	84	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Anaerovirgula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:46,369] [INFO] GTDB search result was written to GCF_016908555.1_ASM1690855v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:46,370] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:46,372] [INFO] DFAST_QC result json was written to GCF_016908555.1_ASM1690855v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:46,372] [INFO] DFAST_QC completed!
[2024-01-25 19:46:46,372] [INFO] Total running time: 0h0m56s