[2024-01-24 11:26:38,978] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg26d54be3-dc9e-44c3-aacf-55c2743b8aca/dqc_reference
[2024-01-24 11:26:40,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,383] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfcacbe6-9d69-4ed6-9845-269da091567d/GCF_004403945.1_ASM440394v1_genomic.fna.gz | prodigal -d GCF_004403945.1_ASM440394v1_genomic.fna/cds.fna -a GCF_004403945.1_ASM440394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:54,418] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:54,418] [INFO] Task started: HMMsearch
[2024-01-24 11:26:54,418] [INFO] Running command: hmmsearch --tblout GCF_004403945.1_ASM440394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26d54be3-dc9e-44c3-aacf-55c2743b8aca/dqc_reference/reference_markers.hmm GCF_004403945.1_ASM440394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:54,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:54,703] [INFO] Found 6/6 markers.
[2024-01-24 11:26:54,748] [INFO] Query marker FASTA was written to GCF_004403945.1_ASM440394v1_genomic.fna/markers.fasta
[2024-01-24 11:26:54,749] [INFO] Task started: Blastn
[2024-01-24 11:26:54,749] [INFO] Running command: blastn -query GCF_004403945.1_ASM440394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26d54be3-dc9e-44c3-aacf-55c2743b8aca/dqc_reference/reference_markers.fasta -out GCF_004403945.1_ASM440394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:55,991] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:55,995] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:55,996] [INFO] Target genome list was writen to GCF_004403945.1_ASM440394v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:56,004] [INFO] Task started: fastANI
[2024-01-24 11:26:56,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfcacbe6-9d69-4ed6-9845-269da091567d/GCF_004403945.1_ASM440394v1_genomic.fna.gz --refList GCF_004403945.1_ASM440394v1_genomic.fna/target_genomes.txt --output GCF_004403945.1_ASM440394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:06,736] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:06,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26d54be3-dc9e-44c3-aacf-55c2743b8aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:06,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26d54be3-dc9e-44c3-aacf-55c2743b8aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:06,751] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:06,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:06,751] [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 zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	88.1329	1028	1530	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	87.0202	1038	1530	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	85.9912	1010	1530	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.4102	547	1530	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.332	548	1530	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	80.8003	598	1530	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.6099	637	1530	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	80.2346	483	1530	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	80.1653	505	1530	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	79.9899	518	1530	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	79.8552	493	1530	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.5075	412	1530	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.2949	417	1530	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.2865	426	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:06,754] [INFO] DFAST Taxonomy check result was written to GCF_004403945.1_ASM440394v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:06,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:06,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:06,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26d54be3-dc9e-44c3-aacf-55c2743b8aca/dqc_reference/checkm_data
[2024-01-24 11:27:06,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:06,804] [INFO] Task started: CheckM
[2024-01-24 11:27:06,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004403945.1_ASM440394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004403945.1_ASM440394v1_genomic.fna/checkm_input GCF_004403945.1_ASM440394v1_genomic.fna/checkm_result
[2024-01-24 11:27:49,773] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:49,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,798] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:49,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:49,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004403945.1_ASM440394v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:49,799] [INFO] Task started: Blastn
[2024-01-24 11:27:49,799] [INFO] Running command: blastn -query GCF_004403945.1_ASM440394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26d54be3-dc9e-44c3-aacf-55c2743b8aca/dqc_reference/reference_markers_gtdb.fasta -out GCF_004403945.1_ASM440394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:51,736] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:51,740] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:51,741] [INFO] Target genome list was writen to GCF_004403945.1_ASM440394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:51,749] [INFO] Task started: fastANI
[2024-01-24 11:27:51,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfcacbe6-9d69-4ed6-9845-269da091567d/GCF_004403945.1_ASM440394v1_genomic.fna.gz --refList GCF_004403945.1_ASM440394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004403945.1_ASM440394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:00,844] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:00,855] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:00,855] [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_004403945.1	s__Cryobacterium sp004403945	100.0	1525	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004210215.1	s__Cryobacterium sp004210215	93.1541	998	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929555.1	s__Cryobacterium sp002929555	88.8319	1047	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909375.1	s__Cryobacterium zongtaii	88.1375	1027	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.98	96.32	0.90	0.86	11	-
GCF_004402695.1	s__Cryobacterium sp004402695	88.0626	954	1530	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	87.3767	1038	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611035.1	s__Cryobacterium soli	87.0083	1039	1530	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	86.0279	1006	1530	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 11:28:00,857] [INFO] GTDB search result was written to GCF_004403945.1_ASM440394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:00,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:00,861] [INFO] DFAST_QC result json was written to GCF_004403945.1_ASM440394v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:00,861] [INFO] DFAST_QC completed!
[2024-01-24 11:28:00,861] [INFO] Total running time: 0h1m22s