[2024-01-24 14:50:04,285] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:04,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:04,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg45649490-665d-4505-b2d0-7e73e653a6e3/dqc_reference
[2024-01-24 14:50:05,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,664] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg1561072c-240a-4771-a21e-4c7229914ea5/GCF_004402785.1_ASM440278v1_genomic.fna.gz | prodigal -d GCF_004402785.1_ASM440278v1_genomic.fna/cds.fna -a GCF_004402785.1_ASM440278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:16,823] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:16,823] [INFO] Task started: HMMsearch
[2024-01-24 14:50:16,824] [INFO] Running command: hmmsearch --tblout GCF_004402785.1_ASM440278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45649490-665d-4505-b2d0-7e73e653a6e3/dqc_reference/reference_markers.hmm GCF_004402785.1_ASM440278v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:17,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:17,081] [INFO] Found 6/6 markers.
[2024-01-24 14:50:17,117] [INFO] Query marker FASTA was written to GCF_004402785.1_ASM440278v1_genomic.fna/markers.fasta
[2024-01-24 14:50:17,117] [INFO] Task started: Blastn
[2024-01-24 14:50:17,118] [INFO] Running command: blastn -query GCF_004402785.1_ASM440278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45649490-665d-4505-b2d0-7e73e653a6e3/dqc_reference/reference_markers.fasta -out GCF_004402785.1_ASM440278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:18,279] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:18,283] [INFO] Selected 18 target genomes.
[2024-01-24 14:50:18,283] [INFO] Target genome list was writen to GCF_004402785.1_ASM440278v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:18,291] [INFO] Task started: fastANI
[2024-01-24 14:50:18,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg1561072c-240a-4771-a21e-4c7229914ea5/GCF_004402785.1_ASM440278v1_genomic.fna.gz --refList GCF_004402785.1_ASM440278v1_genomic.fna/target_genomes.txt --output GCF_004402785.1_ASM440278v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:30,401] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:30,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45649490-665d-4505-b2d0-7e73e653a6e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:30,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45649490-665d-4505-b2d0-7e73e653a6e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:30,413] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:50:30,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:50:30,413] [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	81.6807	710	1198	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.5791	604	1198	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.4901	598	1198	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	80.8397	589	1198	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	80.7383	582	1198	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	80.7201	614	1198	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	79.8363	434	1198	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	79.6894	507	1198	95	below_threshold
Cryobacterium psychrophilum	strain=DSM 4854	GCA_004365915.1	41988	41988	type	True	79.5208	506	1198	95	below_threshold
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	79.4001	495	1198	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3274	396	1198	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.1877	365	1198	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.0164	381	1198	95	below_threshold
Paraoerskovia marina	strain=DSM 21750	GCA_000701465.1	545619	545619	type	True	76.7421	148	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:30,415] [INFO] DFAST Taxonomy check result was written to GCF_004402785.1_ASM440278v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:30,416] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:30,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:30,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45649490-665d-4505-b2d0-7e73e653a6e3/dqc_reference/checkm_data
[2024-01-24 14:50:30,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:30,458] [INFO] Task started: CheckM
[2024-01-24 14:50:30,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004402785.1_ASM440278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004402785.1_ASM440278v1_genomic.fna/checkm_input GCF_004402785.1_ASM440278v1_genomic.fna/checkm_result
[2024-01-24 14:51:04,932] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:04,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:04,953] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:04,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:04,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004402785.1_ASM440278v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:04,954] [INFO] Task started: Blastn
[2024-01-24 14:51:04,954] [INFO] Running command: blastn -query GCF_004402785.1_ASM440278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45649490-665d-4505-b2d0-7e73e653a6e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004402785.1_ASM440278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:06,652] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:06,656] [INFO] Selected 13 target genomes.
[2024-01-24 14:51:06,657] [INFO] Target genome list was writen to GCF_004402785.1_ASM440278v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:06,666] [INFO] Task started: fastANI
[2024-01-24 14:51:06,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg1561072c-240a-4771-a21e-4c7229914ea5/GCF_004402785.1_ASM440278v1_genomic.fna.gz --refList GCF_004402785.1_ASM440278v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004402785.1_ASM440278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:16,989] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:17,005] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:17,005] [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_004402785.1	s__Cryobacterium sp004402785	100.0	1196	1198	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	90.1727	926	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.47	98.47	0.92	0.92	2	-
GCF_004403515.1	s__Cryobacterium sp004403515	90.0459	797	1198	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	89.9927	912	1198	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	83.1147	745	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
GCA_014376815.1	s__Cryobacterium sp014376815	82.9262	632	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403065.1	s__Cryobacterium sp004403065	82.4966	718	1198	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	81.9364	623	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101115.1	s__Cryobacterium psychrotolerans	81.5715	604	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.25	98.21	0.94	0.88	4	-
GCF_000701465.1	s__Paraoerskovia marina	76.7518	147	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Paraoerskovia	95.0	98.25	98.25	0.95	0.95	2	-
GCF_004117855.1	s__Halomonas_C coralii	74.8991	66	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517355.1	s__Ozemobacter sp012517355	74.6806	74	1198	d__Bacteria;p__Riflebacteria;c__Ozemobacteria;o__Ozemobacterales;f__Ozemobacteraceae;g__Ozemobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:17,007] [INFO] GTDB search result was written to GCF_004402785.1_ASM440278v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:17,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:17,012] [INFO] DFAST_QC result json was written to GCF_004402785.1_ASM440278v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:17,012] [INFO] DFAST_QC completed!
[2024-01-24 14:51:17,013] [INFO] Total running time: 0h1m13s