[2024-01-24 13:31:41,356] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:41,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:41,358] [INFO] DQC Reference Directory: /var/lib/cwl/stga4057f7d-ea25-4fc5-ae63-b4a135885e9e/dqc_reference
[2024-01-24 13:31:42,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:42,631] [INFO] Task started: Prodigal
[2024-01-24 13:31:42,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg14100a6a-c666-4524-86bc-7bf56dedc6e5/GCF_004402235.1_ASM440223v1_genomic.fna.gz | prodigal -d GCF_004402235.1_ASM440223v1_genomic.fna/cds.fna -a GCF_004402235.1_ASM440223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:53,558] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:53,558] [INFO] Task started: HMMsearch
[2024-01-24 13:31:53,558] [INFO] Running command: hmmsearch --tblout GCF_004402235.1_ASM440223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4057f7d-ea25-4fc5-ae63-b4a135885e9e/dqc_reference/reference_markers.hmm GCF_004402235.1_ASM440223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:53,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:53,817] [INFO] Found 6/6 markers.
[2024-01-24 13:31:53,865] [INFO] Query marker FASTA was written to GCF_004402235.1_ASM440223v1_genomic.fna/markers.fasta
[2024-01-24 13:31:53,866] [INFO] Task started: Blastn
[2024-01-24 13:31:53,866] [INFO] Running command: blastn -query GCF_004402235.1_ASM440223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4057f7d-ea25-4fc5-ae63-b4a135885e9e/dqc_reference/reference_markers.fasta -out GCF_004402235.1_ASM440223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:55,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:55,141] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:55,141] [INFO] Target genome list was writen to GCF_004402235.1_ASM440223v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:55,339] [INFO] Task started: fastANI
[2024-01-24 13:31:55,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg14100a6a-c666-4524-86bc-7bf56dedc6e5/GCF_004402235.1_ASM440223v1_genomic.fna.gz --refList GCF_004402235.1_ASM440223v1_genomic.fna/target_genomes.txt --output GCF_004402235.1_ASM440223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:04,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:04,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4057f7d-ea25-4fc5-ae63-b4a135885e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:04,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4057f7d-ea25-4fc5-ae63-b4a135885e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:04,477] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:04,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:04,478] [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
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	81.3931	597	1287	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.3184	544	1287	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.3115	533	1287	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	81.1854	608	1287	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	81.162	645	1287	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	80.9984	636	1287	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.3888	585	1287	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	79.6956	478	1287	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	79.6801	483	1287	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.7497	436	1287	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.662	402	1287	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.4446	398	1287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,479] [INFO] DFAST Taxonomy check result was written to GCF_004402235.1_ASM440223v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:04,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:04,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:04,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4057f7d-ea25-4fc5-ae63-b4a135885e9e/dqc_reference/checkm_data
[2024-01-24 13:32:04,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:04,529] [INFO] Task started: CheckM
[2024-01-24 13:32:04,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004402235.1_ASM440223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004402235.1_ASM440223v1_genomic.fna/checkm_input GCF_004402235.1_ASM440223v1_genomic.fna/checkm_result
[2024-01-24 13:32:41,266] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:41,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,294] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:41,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:41,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004402235.1_ASM440223v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:41,296] [INFO] Task started: Blastn
[2024-01-24 13:32:41,296] [INFO] Running command: blastn -query GCF_004402235.1_ASM440223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4057f7d-ea25-4fc5-ae63-b4a135885e9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004402235.1_ASM440223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:43,224] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:43,228] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:43,229] [INFO] Target genome list was writen to GCF_004402235.1_ASM440223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:43,358] [INFO] Task started: fastANI
[2024-01-24 13:32:43,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg14100a6a-c666-4524-86bc-7bf56dedc6e5/GCF_004402235.1_ASM440223v1_genomic.fna.gz --refList GCF_004402235.1_ASM440223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004402235.1_ASM440223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:53,601] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:53,616] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:53,616] [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_004402235.1	s__Cryobacterium sp004402235	100.0	1287	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.29	99.21	0.93	0.91	7	conclusive
GCF_004402485.1	s__Cryobacterium sp004402485	91.6339	1098	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752155.1	s__Cryobacterium sp015752155	82.604	760	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403515.1	s__Cryobacterium sp004403515	82.5287	642	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402495.1	s__Cryobacterium sp004402495	82.5177	750	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.47	98.47	0.92	0.92	2	-
GCF_004402595.1	s__Cryobacterium sp004402595	81.9678	657	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
GCF_004403065.1	s__Cryobacterium sp004403065	81.714	647	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403465.1	s__Cryobacterium sp004403465	81.5843	637	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.40	99.40	0.93	0.93	2	-
GCA_014376815.1	s__Cryobacterium sp014376815	81.5198	567	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402215.1	s__Cryobacterium sp004402215	81.3958	593	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679725.1	s__Cryobacterium arcticum_A	81.1686	662	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185895.1	s__Cryobacterium arcticum	80.981	638	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:53,618] [INFO] GTDB search result was written to GCF_004402235.1_ASM440223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:53,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:53,622] [INFO] DFAST_QC result json was written to GCF_004402235.1_ASM440223v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:53,622] [INFO] DFAST_QC completed!
[2024-01-24 13:32:53,622] [INFO] Total running time: 0h1m12s