[2024-01-24 14:28:08,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c12d119-1fe0-405c-ada6-48a8d37ee33b/dqc_reference
[2024-01-24 14:28:10,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,420] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,420] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd1d5c05-43de-472a-96a2-21c97765c0d2/GCF_004403395.1_ASM440339v1_genomic.fna.gz | prodigal -d GCF_004403395.1_ASM440339v1_genomic.fna/cds.fna -a GCF_004403395.1_ASM440339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:19,732] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:19,732] [INFO] Task started: HMMsearch
[2024-01-24 14:28:19,733] [INFO] Running command: hmmsearch --tblout GCF_004403395.1_ASM440339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c12d119-1fe0-405c-ada6-48a8d37ee33b/dqc_reference/reference_markers.hmm GCF_004403395.1_ASM440339v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:19,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:19,988] [INFO] Found 6/6 markers.
[2024-01-24 14:28:20,033] [INFO] Query marker FASTA was written to GCF_004403395.1_ASM440339v1_genomic.fna/markers.fasta
[2024-01-24 14:28:20,034] [INFO] Task started: Blastn
[2024-01-24 14:28:20,034] [INFO] Running command: blastn -query GCF_004403395.1_ASM440339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c12d119-1fe0-405c-ada6-48a8d37ee33b/dqc_reference/reference_markers.fasta -out GCF_004403395.1_ASM440339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:21,285] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:21,288] [INFO] Selected 11 target genomes.
[2024-01-24 14:28:21,289] [INFO] Target genome list was writen to GCF_004403395.1_ASM440339v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:21,313] [INFO] Task started: fastANI
[2024-01-24 14:28:21,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1d5c05-43de-472a-96a2-21c97765c0d2/GCF_004403395.1_ASM440339v1_genomic.fna.gz --refList GCF_004403395.1_ASM440339v1_genomic.fna/target_genomes.txt --output GCF_004403395.1_ASM440339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:30,517] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:30,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c12d119-1fe0-405c-ada6-48a8d37ee33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:30,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c12d119-1fe0-405c-ada6-48a8d37ee33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:30,531] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:28:30,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:28:30,531] [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	87.2382	821	1034	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	82.1349	578	1034	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	82.0875	580	1034	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	81.7243	552	1034	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	81.6391	595	1034	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	81.4895	587	1034	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.8385	556	1034	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.7681	322	1034	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.6725	348	1034	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.5429	401	1034	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.3492	371	1034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:30,535] [INFO] DFAST Taxonomy check result was written to GCF_004403395.1_ASM440339v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:30,536] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:30,536] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:30,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c12d119-1fe0-405c-ada6-48a8d37ee33b/dqc_reference/checkm_data
[2024-01-24 14:28:30,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:30,576] [INFO] Task started: CheckM
[2024-01-24 14:28:30,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004403395.1_ASM440339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004403395.1_ASM440339v1_genomic.fna/checkm_input GCF_004403395.1_ASM440339v1_genomic.fna/checkm_result
[2024-01-24 14:29:05,779] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:05,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:05,799] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:05,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:05,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004403395.1_ASM440339v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:05,800] [INFO] Task started: Blastn
[2024-01-24 14:29:05,800] [INFO] Running command: blastn -query GCF_004403395.1_ASM440339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c12d119-1fe0-405c-ada6-48a8d37ee33b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004403395.1_ASM440339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:07,623] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:07,627] [INFO] Selected 6 target genomes.
[2024-01-24 14:29:07,627] [INFO] Target genome list was writen to GCF_004403395.1_ASM440339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:07,632] [INFO] Task started: fastANI
[2024-01-24 14:29:07,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1d5c05-43de-472a-96a2-21c97765c0d2/GCF_004403395.1_ASM440339v1_genomic.fna.gz --refList GCF_004403395.1_ASM440339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004403395.1_ASM440339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:13,379] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:13,385] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:13,386] [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_004403395.1	s__Cryobacterium sp004403395	100.0	1032	1034	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_004403465.1	s__Cryobacterium sp004403465	90.4318	850	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.40	99.40	0.93	0.93	2	-
GCF_002929845.1	s__Cryobacterium sp002929845	89.9754	854	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.90	95.88	0.91	0.88	15	-
GCF_004403065.1	s__Cryobacterium sp004403065	88.4343	843	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402375.1	s__Cryobacterium breve	87.2488	821	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004402595.1	s__Cryobacterium sp004402595	85.8535	783	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:13,388] [INFO] GTDB search result was written to GCF_004403395.1_ASM440339v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:13,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:13,391] [INFO] DFAST_QC result json was written to GCF_004403395.1_ASM440339v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:13,392] [INFO] DFAST_QC completed!
[2024-01-24 14:29:13,392] [INFO] Total running time: 0h1m5s