[2024-01-24 11:13:04,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b5a0ce6-3a20-49d6-ab1a-19e7a3b2d9a2/dqc_reference
[2024-01-24 11:13:05,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,601] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c8c2abe-51b3-4391-b4ad-f39062cd6b77/GCF_004403515.1_ASM440351v1_genomic.fna.gz | prodigal -d GCF_004403515.1_ASM440351v1_genomic.fna/cds.fna -a GCF_004403515.1_ASM440351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:15,066] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:15,066] [INFO] Task started: HMMsearch
[2024-01-24 11:13:15,066] [INFO] Running command: hmmsearch --tblout GCF_004403515.1_ASM440351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b5a0ce6-3a20-49d6-ab1a-19e7a3b2d9a2/dqc_reference/reference_markers.hmm GCF_004403515.1_ASM440351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:15,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:15,346] [INFO] Found 6/6 markers.
[2024-01-24 11:13:15,377] [INFO] Query marker FASTA was written to GCF_004403515.1_ASM440351v1_genomic.fna/markers.fasta
[2024-01-24 11:13:15,377] [INFO] Task started: Blastn
[2024-01-24 11:13:15,377] [INFO] Running command: blastn -query GCF_004403515.1_ASM440351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b5a0ce6-3a20-49d6-ab1a-19e7a3b2d9a2/dqc_reference/reference_markers.fasta -out GCF_004403515.1_ASM440351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:16,532] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:16,536] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:16,537] [INFO] Target genome list was writen to GCF_004403515.1_ASM440351v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:16,589] [INFO] Task started: fastANI
[2024-01-24 11:13:16,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c8c2abe-51b3-4391-b4ad-f39062cd6b77/GCF_004403515.1_ASM440351v1_genomic.fna.gz --refList GCF_004403515.1_ASM440351v1_genomic.fna/target_genomes.txt --output GCF_004403515.1_ASM440351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:30,806] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:30,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b5a0ce6-3a20-49d6-ab1a-19e7a3b2d9a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:30,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b5a0ce6-3a20-49d6-ab1a-19e7a3b2d9a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:30,825] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:30,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:30,825] [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	82.7327	698	1081	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	82.2862	596	1081	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	82.2349	613	1081	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	81.6452	588	1081	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	81.589	603	1081	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	81.5256	596	1081	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.5812	572	1081	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	79.9953	524	1081	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	79.9932	523	1081	95	below_threshold
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	79.6753	497	1081	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.836	426	1081	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.618	387	1081	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.5687	397	1081	95	below_threshold
Nakamurella flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	76.0217	156	1081	95	below_threshold
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	75.8011	156	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:30,827] [INFO] DFAST Taxonomy check result was written to GCF_004403515.1_ASM440351v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:30,827] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:30,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:30,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b5a0ce6-3a20-49d6-ab1a-19e7a3b2d9a2/dqc_reference/checkm_data
[2024-01-24 11:13:30,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:30,863] [INFO] Task started: CheckM
[2024-01-24 11:13:30,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004403515.1_ASM440351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004403515.1_ASM440351v1_genomic.fna/checkm_input GCF_004403515.1_ASM440351v1_genomic.fna/checkm_result
[2024-01-24 11:14:03,171] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:03,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:03,195] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:03,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:03,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004403515.1_ASM440351v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:03,197] [INFO] Task started: Blastn
[2024-01-24 11:14:03,197] [INFO] Running command: blastn -query GCF_004403515.1_ASM440351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b5a0ce6-3a20-49d6-ab1a-19e7a3b2d9a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004403515.1_ASM440351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:04,948] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:04,952] [INFO] Selected 12 target genomes.
[2024-01-24 11:14:04,952] [INFO] Target genome list was writen to GCF_004403515.1_ASM440351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:04,960] [INFO] Task started: fastANI
[2024-01-24 11:14:04,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c8c2abe-51b3-4391-b4ad-f39062cd6b77/GCF_004403515.1_ASM440351v1_genomic.fna.gz --refList GCF_004403515.1_ASM440351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004403515.1_ASM440351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:14,823] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:14,835] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:14,835] [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_004403515.1	s__Cryobacterium sp004403515	100.0	1073	1081	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_004402495.1	s__Cryobacterium sp004402495	91.0069	885	1081	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	90.8015	860	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402785.1	s__Cryobacterium sp004402785	89.9238	810	1081	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	84.0549	718	1081	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	83.4548	707	1081	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	82.5912	642	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402485.1	s__Cryobacterium sp004402485	82.4866	649	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403945.1	s__Cryobacterium sp004403945	81.5432	612	1081	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 11:14:14,837] [INFO] GTDB search result was written to GCF_004403515.1_ASM440351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:14,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:14,841] [INFO] DFAST_QC result json was written to GCF_004403515.1_ASM440351v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:14,842] [INFO] DFAST_QC completed!
[2024-01-24 11:14:14,842] [INFO] Total running time: 0h1m10s