[2024-01-24 13:45:45,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,387] [INFO] DQC Reference Directory: /var/lib/cwl/stge21ffd4b-63b1-4bc8-848b-49d9c3e39456/dqc_reference
[2024-01-24 13:45:47,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,057] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,057] [INFO] Running command: gunzip -c /var/lib/cwl/stgff277ff0-b397-4b1c-882e-5e8b70efe63d/GCF_013409745.1_ASM1340974v1_genomic.fna.gz | prodigal -d GCF_013409745.1_ASM1340974v1_genomic.fna/cds.fna -a GCF_013409745.1_ASM1340974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:55,979] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:55,980] [INFO] Task started: HMMsearch
[2024-01-24 13:45:55,980] [INFO] Running command: hmmsearch --tblout GCF_013409745.1_ASM1340974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge21ffd4b-63b1-4bc8-848b-49d9c3e39456/dqc_reference/reference_markers.hmm GCF_013409745.1_ASM1340974v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:56,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:56,245] [INFO] Found 6/6 markers.
[2024-01-24 13:45:56,281] [INFO] Query marker FASTA was written to GCF_013409745.1_ASM1340974v1_genomic.fna/markers.fasta
[2024-01-24 13:45:56,282] [INFO] Task started: Blastn
[2024-01-24 13:45:56,282] [INFO] Running command: blastn -query GCF_013409745.1_ASM1340974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge21ffd4b-63b1-4bc8-848b-49d9c3e39456/dqc_reference/reference_markers.fasta -out GCF_013409745.1_ASM1340974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:57,554] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:57,558] [INFO] Selected 20 target genomes.
[2024-01-24 13:45:57,559] [INFO] Target genome list was writen to GCF_013409745.1_ASM1340974v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:57,611] [INFO] Task started: fastANI
[2024-01-24 13:45:57,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgff277ff0-b397-4b1c-882e-5e8b70efe63d/GCF_013409745.1_ASM1340974v1_genomic.fna.gz --refList GCF_013409745.1_ASM1340974v1_genomic.fna/target_genomes.txt --output GCF_013409745.1_ASM1340974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:10,141] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:10,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge21ffd4b-63b1-4bc8-848b-49d9c3e39456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:10,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge21ffd4b-63b1-4bc8-848b-49d9c3e39456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:10,167] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:10,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:10,167] [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 pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	100.0	971	971	95	conclusive
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	81.4563	543	971	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.2103	509	971	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	81.1304	526	971	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.1028	551	971	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	81.029	506	971	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	80.993	457	971	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	80.7782	493	971	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	80.7254	498	971	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	80.7014	492	971	95	below_threshold
Microbacterium ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	80.6997	485	971	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	80.6808	475	971	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	80.5806	477	971	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	80.1119	431	971	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.0438	455	971	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	79.9636	424	971	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	79.9376	426	971	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.8415	408	971	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.8248	408	971	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.6269	411	971	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:10,169] [INFO] DFAST Taxonomy check result was written to GCF_013409745.1_ASM1340974v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:10,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:10,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:10,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge21ffd4b-63b1-4bc8-848b-49d9c3e39456/dqc_reference/checkm_data
[2024-01-24 13:46:10,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:10,205] [INFO] Task started: CheckM
[2024-01-24 13:46:10,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409745.1_ASM1340974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409745.1_ASM1340974v1_genomic.fna/checkm_input GCF_013409745.1_ASM1340974v1_genomic.fna/checkm_result
[2024-01-24 13:47:02,886] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:02,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,914] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:02,914] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:02,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409745.1_ASM1340974v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:02,915] [INFO] Task started: Blastn
[2024-01-24 13:47:02,915] [INFO] Running command: blastn -query GCF_013409745.1_ASM1340974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge21ffd4b-63b1-4bc8-848b-49d9c3e39456/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409745.1_ASM1340974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:04,866] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:04,869] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:04,869] [INFO] Target genome list was writen to GCF_013409745.1_ASM1340974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:04,885] [INFO] Task started: fastANI
[2024-01-24 13:47:04,885] [INFO] Running command: fastANI --query /var/lib/cwl/stgff277ff0-b397-4b1c-882e-5e8b70efe63d/GCF_013409745.1_ASM1340974v1_genomic.fna.gz --refList GCF_013409745.1_ASM1340974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409745.1_ASM1340974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:19,407] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:19,427] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:19,428] [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_013409745.1	s__Microbacterium pseudoresistens	100.0	971	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_903645325.1	s__Microbacterium sp903645325	81.6018	513	971	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	81.4954	540	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_015040615.1	s__Microbacterium sp015040615	81.4934	536	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506375.1	s__Microbacterium sp902506375	81.4905	553	971	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	81.3897	498	971	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	81.3556	501	971	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	81.3461	558	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
GCA_017306305.1	s__Microbacterium sp017306305	81.3321	570	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCA_002257455.1	s__Microbacterium sp002257455	81.2725	518	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752045.1	s__Microbacterium sp001639925	81.195	540	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.61	99.21	0.98	0.97	3	-
GCF_001552355.1	s__Microbacterium resistens	81.147	524	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387575.1	s__Microbacterium sp003387575	81.0941	552	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002837415.1	s__Microbacterium sp002837415	81.0265	504	971	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	80.9794	537	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084045.1	s__Microbacterium esteraromaticum_D	80.9204	512	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008868125.1	s__Microbacterium maritypicum	80.6152	504	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.89	96.90	0.89	0.86	8	-
GCF_004564075.1	s__Microbacterium sediminis	80.1256	430	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_001426925.1	s__Microbacterium sp001426925	80.0061	420	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:19,430] [INFO] GTDB search result was written to GCF_013409745.1_ASM1340974v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:19,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:19,435] [INFO] DFAST_QC result json was written to GCF_013409745.1_ASM1340974v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:19,435] [INFO] DFAST_QC completed!
[2024-01-24 13:47:19,435] [INFO] Total running time: 0h1m34s