[2024-01-24 13:32:55,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:55,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:55,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4517968-bac4-4938-bdbf-bd20635bfa6d/dqc_reference
[2024-01-24 13:32:57,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,039] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,040] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc604433-0242-4fb2-bd35-1f6b83301ea8/GCF_001552355.1_ASM155235v1_genomic.fna.gz | prodigal -d GCF_001552355.1_ASM155235v1_genomic.fna/cds.fna -a GCF_001552355.1_ASM155235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:07,084] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:07,084] [INFO] Task started: HMMsearch
[2024-01-24 13:33:07,085] [INFO] Running command: hmmsearch --tblout GCF_001552355.1_ASM155235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4517968-bac4-4938-bdbf-bd20635bfa6d/dqc_reference/reference_markers.hmm GCF_001552355.1_ASM155235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:07,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:07,338] [INFO] Found 6/6 markers.
[2024-01-24 13:33:07,375] [INFO] Query marker FASTA was written to GCF_001552355.1_ASM155235v1_genomic.fna/markers.fasta
[2024-01-24 13:33:07,375] [INFO] Task started: Blastn
[2024-01-24 13:33:07,375] [INFO] Running command: blastn -query GCF_001552355.1_ASM155235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4517968-bac4-4938-bdbf-bd20635bfa6d/dqc_reference/reference_markers.fasta -out GCF_001552355.1_ASM155235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:08,741] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:08,744] [INFO] Selected 18 target genomes.
[2024-01-24 13:33:08,744] [INFO] Target genome list was writen to GCF_001552355.1_ASM155235v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:08,758] [INFO] Task started: fastANI
[2024-01-24 13:33:08,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc604433-0242-4fb2-bd35-1f6b83301ea8/GCF_001552355.1_ASM155235v1_genomic.fna.gz --refList GCF_001552355.1_ASM155235v1_genomic.fna/target_genomes.txt --output GCF_001552355.1_ASM155235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:21,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:21,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4517968-bac4-4938-bdbf-bd20635bfa6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:21,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4517968-bac4-4938-bdbf-bd20635bfa6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:21,196] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:21,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:21,197] [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
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	100.0	1204	1215	95	conclusive
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	81.3468	632	1215	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	81.3126	500	1215	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	81.1463	539	1215	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	81.0967	594	1215	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.8249	583	1215	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.6682	497	1215	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	80.5137	497	1215	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	80.471	505	1215	95	below_threshold
Microbacterium keratanolyticum	strain=DSM 8606	GCA_016907255.1	67574	67574	type	True	80.1717	462	1215	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	79.5849	425	1215	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	79.5685	456	1215	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.4884	457	1215	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	79.4472	417	1215	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	79.4472	417	1215	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.2766	440	1215	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.2281	405	1215	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.2036	404	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:21,198] [INFO] DFAST Taxonomy check result was written to GCF_001552355.1_ASM155235v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:21,199] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:21,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:21,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4517968-bac4-4938-bdbf-bd20635bfa6d/dqc_reference/checkm_data
[2024-01-24 13:33:21,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:21,241] [INFO] Task started: CheckM
[2024-01-24 13:33:21,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552355.1_ASM155235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552355.1_ASM155235v1_genomic.fna/checkm_input GCF_001552355.1_ASM155235v1_genomic.fna/checkm_result
[2024-01-24 13:34:08,160] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:08,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:08,178] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:08,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:08,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552355.1_ASM155235v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:08,179] [INFO] Task started: Blastn
[2024-01-24 13:34:08,179] [INFO] Running command: blastn -query GCF_001552355.1_ASM155235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4517968-bac4-4938-bdbf-bd20635bfa6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552355.1_ASM155235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:10,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:10,330] [INFO] Selected 18 target genomes.
[2024-01-24 13:34:10,330] [INFO] Target genome list was writen to GCF_001552355.1_ASM155235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:10,354] [INFO] Task started: fastANI
[2024-01-24 13:34:10,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc604433-0242-4fb2-bd35-1f6b83301ea8/GCF_001552355.1_ASM155235v1_genomic.fna.gz --refList GCF_001552355.1_ASM155235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552355.1_ASM155235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:23,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:23,260] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:23,260] [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_001552355.1	s__Microbacterium resistens	100.0	1204	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002257455.1	s__Microbacterium sp002257455	81.6086	572	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268435.1	s__Microbacterium sp018268435	81.6036	511	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268455.1	s__Microbacterium sp018268455	81.5011	535	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306305.1	s__Microbacterium sp017306305	81.469	621	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCF_902506375.1	s__Microbacterium sp902506375	81.405	621	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956545.1	s__Microbacterium azadirachtae	81.3609	630	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_013409745.1	s__Microbacterium pseudoresistens	81.339	498	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956505.1	s__Microbacterium azadirachtae_A	81.2802	639	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
GCA_018268515.1	s__Microbacterium sp018268515	81.205	588	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015040615.1	s__Microbacterium sp015040615	81.0093	550	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794315.1	s__Microbacterium sp004794315	80.9904	609	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.84	0.93	0.91	3	-
GCF_002705755.3	s__Microbacterium esteraromaticum_A	80.9319	499	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCF_903645325.1	s__Microbacterium sp903645325	80.9131	500	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758255.1	s__Microbacterium sp009758255	80.8984	586	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794515.1	s__Microbacterium sp004794515	80.5747	563	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003610275.1	s__Microbacterium ginsengiterrae_A	80.3425	546	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564075.1	s__Microbacterium sediminis	79.6208	422	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:23,262] [INFO] GTDB search result was written to GCF_001552355.1_ASM155235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:23,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:23,266] [INFO] DFAST_QC result json was written to GCF_001552355.1_ASM155235v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:23,267] [INFO] DFAST_QC completed!
[2024-01-24 13:34:23,267] [INFO] Total running time: 0h1m28s