[2024-01-24 14:05:00,603] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgb886b052-6a4d-4e44-8d3b-fbffe6a3cabc/dqc_reference
[2024-01-24 14:05:01,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,744] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e8daf35-f00b-4af4-b2bb-65c4ec3703a4/GCF_004564325.1_ASM456432v1_genomic.fna.gz | prodigal -d GCF_004564325.1_ASM456432v1_genomic.fna/cds.fna -a GCF_004564325.1_ASM456432v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:10,599] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:10,599] [INFO] Task started: HMMsearch
[2024-01-24 14:05:10,599] [INFO] Running command: hmmsearch --tblout GCF_004564325.1_ASM456432v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb886b052-6a4d-4e44-8d3b-fbffe6a3cabc/dqc_reference/reference_markers.hmm GCF_004564325.1_ASM456432v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:10,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:10,801] [INFO] Found 6/6 markers.
[2024-01-24 14:05:10,829] [INFO] Query marker FASTA was written to GCF_004564325.1_ASM456432v1_genomic.fna/markers.fasta
[2024-01-24 14:05:10,830] [INFO] Task started: Blastn
[2024-01-24 14:05:10,830] [INFO] Running command: blastn -query GCF_004564325.1_ASM456432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb886b052-6a4d-4e44-8d3b-fbffe6a3cabc/dqc_reference/reference_markers.fasta -out GCF_004564325.1_ASM456432v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:11,949] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:11,954] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:11,954] [INFO] Target genome list was writen to GCF_004564325.1_ASM456432v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:11,972] [INFO] Task started: fastANI
[2024-01-24 14:05:11,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e8daf35-f00b-4af4-b2bb-65c4ec3703a4/GCF_004564325.1_ASM456432v1_genomic.fna.gz --refList GCF_004564325.1_ASM456432v1_genomic.fna/target_genomes.txt --output GCF_004564325.1_ASM456432v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:21,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:21,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb886b052-6a4d-4e44-8d3b-fbffe6a3cabc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:21,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb886b052-6a4d-4e44-8d3b-fbffe6a3cabc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:21,384] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:05:21,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:21,384] [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 psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	100.0	1056	1058	95	conclusive
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	99.9818	1051	1058	95	conclusive
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	81.415	544	1058	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	81.4011	563	1058	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	81.333	527	1058	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	81.1862	558	1058	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	80.771	456	1058	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.6689	559	1058	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	79.9106	523	1058	95	below_threshold
Cryobacterium roopkundense	strain=RuG17	GCA_000764165.1	1001240	1001240	type	True	79.9055	486	1058	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.162	455	1058	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.8612	405	1058	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.6269	415	1058	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:21,388] [INFO] DFAST Taxonomy check result was written to GCF_004564325.1_ASM456432v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:21,388] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:21,388] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:21,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb886b052-6a4d-4e44-8d3b-fbffe6a3cabc/dqc_reference/checkm_data
[2024-01-24 14:05:21,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:21,421] [INFO] Task started: CheckM
[2024-01-24 14:05:21,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004564325.1_ASM456432v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004564325.1_ASM456432v1_genomic.fna/checkm_input GCF_004564325.1_ASM456432v1_genomic.fna/checkm_result
[2024-01-24 14:05:52,014] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:52,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:52,046] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:52,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:52,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004564325.1_ASM456432v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:52,047] [INFO] Task started: Blastn
[2024-01-24 14:05:52,047] [INFO] Running command: blastn -query GCF_004564325.1_ASM456432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb886b052-6a4d-4e44-8d3b-fbffe6a3cabc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004564325.1_ASM456432v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:53,866] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:53,869] [INFO] Selected 14 target genomes.
[2024-01-24 14:05:53,869] [INFO] Target genome list was writen to GCF_004564325.1_ASM456432v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:53,955] [INFO] Task started: fastANI
[2024-01-24 14:05:53,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e8daf35-f00b-4af4-b2bb-65c4ec3703a4/GCF_004564325.1_ASM456432v1_genomic.fna.gz --refList GCF_004564325.1_ASM456432v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004564325.1_ASM456432v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:04,851] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:04,863] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:04,864] [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_900101115.1	s__Cryobacterium psychrotolerans	99.9818	1051	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.25	98.21	0.94	0.88	4	conclusive
GCF_004402215.1	s__Cryobacterium sp004402215	90.8719	872	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404115.1	s__Cryobacterium sp002404115	84.0653	376	1058	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	82.4975	632	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.47	98.47	0.92	0.92	2	-
GCF_015752155.1	s__Cryobacterium sp015752155	82.279	669	1058	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	82.2481	600	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403395.1	s__Cryobacterium sp004403395	82.2052	572	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402595.1	s__Cryobacterium sp004402595	82.1116	625	1058	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	81.8712	606	1058	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	81.666	550	1058	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	81.6327	556	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376815.1	s__Cryobacterium sp014376815	81.5831	528	1058	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	81.3963	563	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403305.1	s__Cryobacterium sp004403305	80.6934	526	1058	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 14:06:04,865] [INFO] GTDB search result was written to GCF_004564325.1_ASM456432v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:04,866] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:04,869] [INFO] DFAST_QC result json was written to GCF_004564325.1_ASM456432v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:04,869] [INFO] DFAST_QC completed!
[2024-01-24 14:06:04,869] [INFO] Total running time: 0h1m4s