[2024-01-24 12:44:52,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,536] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1a4d354-92eb-4ac5-bef6-607125a44b5a/dqc_reference
[2024-01-24 12:44:53,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,836] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,836] [INFO] Running command: gunzip -c /var/lib/cwl/stge3cb5259-ba81-4ab0-8c43-10399fccd512/GCF_024168445.1_ASM2416844v1_genomic.fna.gz | prodigal -d GCF_024168445.1_ASM2416844v1_genomic.fna/cds.fna -a GCF_024168445.1_ASM2416844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:04,354] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:04,354] [INFO] Task started: HMMsearch
[2024-01-24 12:45:04,354] [INFO] Running command: hmmsearch --tblout GCF_024168445.1_ASM2416844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1a4d354-92eb-4ac5-bef6-607125a44b5a/dqc_reference/reference_markers.hmm GCF_024168445.1_ASM2416844v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:04,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:04,635] [INFO] Found 6/6 markers.
[2024-01-24 12:45:04,676] [INFO] Query marker FASTA was written to GCF_024168445.1_ASM2416844v1_genomic.fna/markers.fasta
[2024-01-24 12:45:04,676] [INFO] Task started: Blastn
[2024-01-24 12:45:04,676] [INFO] Running command: blastn -query GCF_024168445.1_ASM2416844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1a4d354-92eb-4ac5-bef6-607125a44b5a/dqc_reference/reference_markers.fasta -out GCF_024168445.1_ASM2416844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:05,797] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:05,801] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:05,801] [INFO] Target genome list was writen to GCF_024168445.1_ASM2416844v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:05,808] [INFO] Task started: fastANI
[2024-01-24 12:45:05,808] [INFO] Running command: fastANI --query /var/lib/cwl/stge3cb5259-ba81-4ab0-8c43-10399fccd512/GCF_024168445.1_ASM2416844v1_genomic.fna.gz --refList GCF_024168445.1_ASM2416844v1_genomic.fna/target_genomes.txt --output GCF_024168445.1_ASM2416844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:16,773] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:16,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1a4d354-92eb-4ac5-bef6-607125a44b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:16,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1a4d354-92eb-4ac5-bef6-607125a44b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:16,786] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:16,786] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:16,786] [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 foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	94.2535	1039	1153	95	below_threshold
Microbacterium foliorum	strain=DSM 12966	GCA_000956415.1	104336	104336	suspected-type	True	94.218	1016	1153	95	below_threshold
Microbacterium phyllosphaerae	strain=DSM 13468	GCA_017876435.1	124798	124798	type	True	86.3814	919	1153	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	85.3768	831	1153	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	85.3571	871	1153	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	83.1608	714	1153	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	83.1526	717	1153	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	83.1023	766	1153	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	82.9763	776	1153	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.3514	561	1153	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	79.7406	505	1153	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	79.7248	514	1153	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.6764	454	1153	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.3088	461	1153	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:16,788] [INFO] DFAST Taxonomy check result was written to GCF_024168445.1_ASM2416844v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:16,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:16,789] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:16,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1a4d354-92eb-4ac5-bef6-607125a44b5a/dqc_reference/checkm_data
[2024-01-24 12:45:16,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:16,827] [INFO] Task started: CheckM
[2024-01-24 12:45:16,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024168445.1_ASM2416844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024168445.1_ASM2416844v1_genomic.fna/checkm_input GCF_024168445.1_ASM2416844v1_genomic.fna/checkm_result
[2024-01-24 12:46:16,163] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:16,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:16,188] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:16,188] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:16,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024168445.1_ASM2416844v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:16,189] [INFO] Task started: Blastn
[2024-01-24 12:46:16,189] [INFO] Running command: blastn -query GCF_024168445.1_ASM2416844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1a4d354-92eb-4ac5-bef6-607125a44b5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024168445.1_ASM2416844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:17,922] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:17,931] [INFO] Selected 16 target genomes.
[2024-01-24 12:46:17,931] [INFO] Target genome list was writen to GCF_024168445.1_ASM2416844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:17,949] [INFO] Task started: fastANI
[2024-01-24 12:46:17,950] [INFO] Running command: fastANI --query /var/lib/cwl/stge3cb5259-ba81-4ab0-8c43-10399fccd512/GCF_024168445.1_ASM2416844v1_genomic.fna.gz --refList GCF_024168445.1_ASM2416844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024168445.1_ASM2416844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:31,710] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:31,728] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:31,729] [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_001426995.1	s__Microbacterium sp001426995	97.9057	1069	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.85	97.85	0.92	0.92	2	conclusive
GCF_003367705.1	s__Microbacterium foliorum	94.24	1040	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001423615.1	s__Microbacterium sp001423615	86.4454	921	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.40	98.40	0.90	0.90	2	-
GCF_017876435.1	s__Microbacterium phyllosphaerae	86.3814	919	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423485.1	s__Microbacterium sp001423485	86.3661	902	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002024885.1	s__Microbacterium foliorum_A	85.6212	900	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	97.34	0.94	0.92	3	-
GCF_001889265.1	s__Microbacterium sp001889265	85.595	880	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.81	98.68	0.92	0.91	4	-
GCF_900105205.1	s__Microbacterium hydrocarbonoxydans	85.3715	869	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015354505.1	s__Microbacterium sp015354505	85.2016	864	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904831005.1	s__Microbacterium hydrocarbonoxydans_B	84.3939	862	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001049495.1	s__Microbacterium sp001049495	84.3526	803	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007667425.1	s__Microbacterium sp007667425	83.8188	789	1153	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	83.3161	741	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900095745.1	s__Microbacterium oxydans_B	83.1416	745	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.33	97.96	0.92	0.90	3	-
GCF_002979655.1	s__Microbacterium sp002979655	83.139	758	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.69	97.67	0.91	0.90	5	-
GCF_002979475.1	s__Microbacterium sp002979475	83.0471	738	1153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:31,730] [INFO] GTDB search result was written to GCF_024168445.1_ASM2416844v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:31,731] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:31,734] [INFO] DFAST_QC result json was written to GCF_024168445.1_ASM2416844v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:31,735] [INFO] DFAST_QC completed!
[2024-01-24 12:46:31,735] [INFO] Total running time: 0h1m39s