[2024-01-24 14:21:47,157] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:47,161] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:47,161] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe58a139-2edd-4b1b-bee0-83f15311d6fd/dqc_reference
[2024-01-24 14:21:48,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:48,443] [INFO] Task started: Prodigal
[2024-01-24 14:21:48,443] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9d3b679-6a44-4e55-86a4-eb3e36b73c44/GCF_006539765.1_ASM653976v1_genomic.fna.gz | prodigal -d GCF_006539765.1_ASM653976v1_genomic.fna/cds.fna -a GCF_006539765.1_ASM653976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:21:58,549] [INFO] Task succeeded: Prodigal
[2024-01-24 14:21:58,549] [INFO] Task started: HMMsearch
[2024-01-24 14:21:58,549] [INFO] Running command: hmmsearch --tblout GCF_006539765.1_ASM653976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe58a139-2edd-4b1b-bee0-83f15311d6fd/dqc_reference/reference_markers.hmm GCF_006539765.1_ASM653976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:21:58,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:21:58,878] [INFO] Found 6/6 markers.
[2024-01-24 14:21:58,909] [INFO] Query marker FASTA was written to GCF_006539765.1_ASM653976v1_genomic.fna/markers.fasta
[2024-01-24 14:21:58,909] [INFO] Task started: Blastn
[2024-01-24 14:21:58,910] [INFO] Running command: blastn -query GCF_006539765.1_ASM653976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe58a139-2edd-4b1b-bee0-83f15311d6fd/dqc_reference/reference_markers.fasta -out GCF_006539765.1_ASM653976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:00,141] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:00,146] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:00,146] [INFO] Target genome list was writen to GCF_006539765.1_ASM653976v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:00,153] [INFO] Task started: fastANI
[2024-01-24 14:22:00,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d3b679-6a44-4e55-86a4-eb3e36b73c44/GCF_006539765.1_ASM653976v1_genomic.fna.gz --refList GCF_006539765.1_ASM653976v1_genomic.fna/target_genomes.txt --output GCF_006539765.1_ASM653976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:08,888] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:08,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe58a139-2edd-4b1b-bee0-83f15311d6fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:08,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe58a139-2edd-4b1b-bee0-83f15311d6fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:08,898] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:08,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:08,898] [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 liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	100.0	1070	1075	95	conclusive
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	99.9984	1073	1075	95	conclusive
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	87.8481	872	1075	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	87.7994	872	1075	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	85.6896	809	1075	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	83.0721	709	1075	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.182	567	1075	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.1251	550	1075	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.6412	431	1075	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.6117	449	1075	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.5835	408	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:08,900] [INFO] DFAST Taxonomy check result was written to GCF_006539765.1_ASM653976v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:08,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:08,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:08,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe58a139-2edd-4b1b-bee0-83f15311d6fd/dqc_reference/checkm_data
[2024-01-24 14:22:08,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:08,939] [INFO] Task started: CheckM
[2024-01-24 14:22:08,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539765.1_ASM653976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539765.1_ASM653976v1_genomic.fna/checkm_input GCF_006539765.1_ASM653976v1_genomic.fna/checkm_result
[2024-01-24 14:22:59,518] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:59,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:59,633] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:59,633] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:59,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539765.1_ASM653976v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:59,634] [INFO] Task started: Blastn
[2024-01-24 14:22:59,634] [INFO] Running command: blastn -query GCF_006539765.1_ASM653976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe58a139-2edd-4b1b-bee0-83f15311d6fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539765.1_ASM653976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:01,504] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:01,508] [INFO] Selected 10 target genomes.
[2024-01-24 14:23:01,509] [INFO] Target genome list was writen to GCF_006539765.1_ASM653976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:01,519] [INFO] Task started: fastANI
[2024-01-24 14:23:01,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d3b679-6a44-4e55-86a4-eb3e36b73c44/GCF_006539765.1_ASM653976v1_genomic.fna.gz --refList GCF_006539765.1_ASM653976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539765.1_ASM653976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:10,588] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:10,606] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:10,607] [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
GCA_008868125.1	s__Microbacterium maritypicum	97.8737	929	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.89	96.90	0.89	0.86	8	conclusive
GCF_000455825.1	s__Microbacterium maritypicum_A	88.8031	867	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.67	97.88	0.89	0.87	11	-
GCF_000425985.1	s__Microbacterium sp000425985	87.8501	871	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.44	96.40	0.87	0.86	7	-
GCF_006540085.1	s__Microbacterium oxydans	87.8042	872	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.85	98.27	0.91	0.87	12	-
GCF_002979475.1	s__Microbacterium sp002979475	87.6625	850	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956405.1	s__Microbacterium oxydans_C	87.2885	813	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979435.1	s__Microbacterium sp002979435	87.0031	817	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979655.1	s__Microbacterium sp002979655	86.5231	816	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.69	97.67	0.91	0.90	5	-
GCF_900095745.1	s__Microbacterium oxydans_B	86.4823	823	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.33	97.96	0.92	0.90	3	-
GCF_004794515.1	s__Microbacterium sp004794515	86.4539	819	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:10,609] [INFO] GTDB search result was written to GCF_006539765.1_ASM653976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:10,610] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:10,614] [INFO] DFAST_QC result json was written to GCF_006539765.1_ASM653976v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:10,615] [INFO] DFAST_QC completed!
[2024-01-24 14:23:10,615] [INFO] Total running time: 0h1m23s