[2024-01-25 20:18:21,150] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:21,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:21,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fdfdbc7-701c-4d4a-bbb4-bb83ef1424ed/dqc_reference
[2024-01-25 20:18:22,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:22,265] [INFO] Task started: Prodigal
[2024-01-25 20:18:22,265] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f5b2fc6-8511-4814-91eb-d825e43854eb/GCF_025028335.1_ASM2502833v1_genomic.fna.gz | prodigal -d GCF_025028335.1_ASM2502833v1_genomic.fna/cds.fna -a GCF_025028335.1_ASM2502833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:29,645] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:29,646] [INFO] Task started: HMMsearch
[2024-01-25 20:18:29,646] [INFO] Running command: hmmsearch --tblout GCF_025028335.1_ASM2502833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fdfdbc7-701c-4d4a-bbb4-bb83ef1424ed/dqc_reference/reference_markers.hmm GCF_025028335.1_ASM2502833v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:29,843] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:29,843] [INFO] Found 6/6 markers.
[2024-01-25 20:18:29,868] [INFO] Query marker FASTA was written to GCF_025028335.1_ASM2502833v1_genomic.fna/markers.fasta
[2024-01-25 20:18:29,869] [INFO] Task started: Blastn
[2024-01-25 20:18:29,869] [INFO] Running command: blastn -query GCF_025028335.1_ASM2502833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fdfdbc7-701c-4d4a-bbb4-bb83ef1424ed/dqc_reference/reference_markers.fasta -out GCF_025028335.1_ASM2502833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:30,966] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:30,973] [INFO] Selected 17 target genomes.
[2024-01-25 20:18:30,974] [INFO] Target genome list was writen to GCF_025028335.1_ASM2502833v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:30,994] [INFO] Task started: fastANI
[2024-01-25 20:18:30,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5b2fc6-8511-4814-91eb-d825e43854eb/GCF_025028335.1_ASM2502833v1_genomic.fna.gz --refList GCF_025028335.1_ASM2502833v1_genomic.fna/target_genomes.txt --output GCF_025028335.1_ASM2502833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:42,715] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:42,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fdfdbc7-701c-4d4a-bbb4-bb83ef1424ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:42,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fdfdbc7-701c-4d4a-bbb4-bb83ef1424ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:42,725] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:18:42,725] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:18:42,725] [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
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	81.1633	471	888	95	below_threshold
Brachybacterium muris	strain=DSM 15460	GCA_016907455.1	219301	219301	type	True	80.6692	485	888	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	80.507	498	888	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	80.3455	428	888	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	80.344	479	888	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	79.9647	458	888	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	79.7667	438	888	95	below_threshold
Brachybacterium endophyticum	strain=M1HQ-2	GCA_003130585.1	2182385	2182385	type	True	79.7601	391	888	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	79.7493	432	888	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	79.6721	429	888	95	below_threshold
Brachybacterium subflavum	strain=CFH 10395	GCA_009299795.1	2585206	2585206	type	True	79.591	424	888	95	below_threshold
Brachybacterium vulturis	strain=VM2412	GCA_002407185.1	2017484	2017484	type	True	79.5889	457	888	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	79.5478	404	888	95	below_threshold
Brachybacterium avium	strain=VR2415	GCA_002216795.1	2017485	2017485	type	True	79.3912	422	888	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.6315	216	888	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.0355	214	888	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.8062	198	888	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:42,727] [INFO] DFAST Taxonomy check result was written to GCF_025028335.1_ASM2502833v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:42,727] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:42,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:42,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fdfdbc7-701c-4d4a-bbb4-bb83ef1424ed/dqc_reference/checkm_data
[2024-01-25 20:18:42,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:42,761] [INFO] Task started: CheckM
[2024-01-25 20:18:42,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025028335.1_ASM2502833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025028335.1_ASM2502833v1_genomic.fna/checkm_input GCF_025028335.1_ASM2502833v1_genomic.fna/checkm_result
[2024-01-25 20:19:43,401] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:43,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:43,419] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:43,420] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:43,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025028335.1_ASM2502833v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:43,421] [INFO] Task started: Blastn
[2024-01-25 20:19:43,421] [INFO] Running command: blastn -query GCF_025028335.1_ASM2502833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fdfdbc7-701c-4d4a-bbb4-bb83ef1424ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_025028335.1_ASM2502833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:45,131] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:45,135] [INFO] Selected 15 target genomes.
[2024-01-25 20:19:45,136] [INFO] Target genome list was writen to GCF_025028335.1_ASM2502833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:45,145] [INFO] Task started: fastANI
[2024-01-25 20:19:45,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5b2fc6-8511-4814-91eb-d825e43854eb/GCF_025028335.1_ASM2502833v1_genomic.fna.gz --refList GCF_025028335.1_ASM2502833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025028335.1_ASM2502833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:55,293] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:55,302] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:19:55,302] [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_015209585.1	s__Brachybacterium sp015209585	81.1468	469	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907455.1	s__Brachybacterium muris	80.694	482	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	97.23	96.65	0.88	0.85	3	-
GCF_000225825.1	s__Brachybacterium squillarum	80.5187	497	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204755.1	s__Brachybacterium aquaticum	80.416	476	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163655.1	s__Brachybacterium nesterenkovii	80.3457	428	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576425.1	s__Brachybacterium phenoliresistens	80.0367	451	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023405.1	s__Brachybacterium faecium	79.942	460	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871795.1	s__Brachybacterium sp002871795	79.8697	418	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005490785.1	s__Brachybacterium sp005490785	79.7742	446	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130585.1	s__Brachybacterium endophyticum	79.7584	391	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299795.1	s__Brachybacterium subflavum	79.5918	424	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347015.1	s__Brachybacterium sp003347015	79.5593	434	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623465.1	s__Brachybacterium halotolerans	79.554	403	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216795.1	s__Brachybacterium avium	79.4425	422	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014897585.1	s__Brachybacterium tyrofermentans	79.2553	423	888	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	97.83	97.83	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:55,303] [INFO] GTDB search result was written to GCF_025028335.1_ASM2502833v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:55,304] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:55,307] [INFO] DFAST_QC result json was written to GCF_025028335.1_ASM2502833v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:55,307] [INFO] DFAST_QC completed!
[2024-01-25 20:19:55,307] [INFO] Total running time: 0h1m34s