[2024-01-24 14:11:46,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c4e76c8-a7f4-44ba-aab0-5c9ea76dc52b/dqc_reference
[2024-01-24 14:11:48,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,879] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cc0b11f-c079-4241-b91f-89bc6818016b/GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/cds.fna -a GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:00,007] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:00,008] [INFO] Task started: HMMsearch
[2024-01-24 14:12:00,008] [INFO] Running command: hmmsearch --tblout GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c4e76c8-a7f4-44ba-aab0-5c9ea76dc52b/dqc_reference/reference_markers.hmm GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:00,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:00,400] [INFO] Found 6/6 markers.
[2024-01-24 14:12:00,452] [INFO] Query marker FASTA was written to GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:00,453] [INFO] Task started: Blastn
[2024-01-24 14:12:00,453] [INFO] Running command: blastn -query GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c4e76c8-a7f4-44ba-aab0-5c9ea76dc52b/dqc_reference/reference_markers.fasta -out GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:01,836] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:01,839] [INFO] Selected 15 target genomes.
[2024-01-24 14:12:01,840] [INFO] Target genome list was writen to GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:01,844] [INFO] Task started: fastANI
[2024-01-24 14:12:01,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cc0b11f-c079-4241-b91f-89bc6818016b/GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna.gz --refList GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:14,788] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:14,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c4e76c8-a7f4-44ba-aab0-5c9ea76dc52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:14,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c4e76c8-a7f4-44ba-aab0-5c9ea76dc52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:14,802] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:12:14,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:14,803] [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 hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	100.0	1190	1193	95	conclusive
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	99.92	1100	1193	95	conclusive
Microbacterium phyllosphaerae	strain=DSM 13468	GCA_017876435.1	124798	124798	type	True	86.0362	917	1193	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	85.1434	866	1193	95	below_threshold
Microbacterium foliorum	strain=DSM 12966	GCA_000956415.1	104336	104336	suspected-type	True	85.1256	850	1193	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	83.0265	783	1193	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	82.9895	756	1193	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	82.9833	765	1193	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	82.9532	668	1193	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	82.8867	757	1193	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.1873	578	1193	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.0951	610	1193	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.0337	485	1193	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.817	452	1193	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.601	487	1193	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:14,804] [INFO] DFAST Taxonomy check result was written to GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:14,805] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:14,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:14,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c4e76c8-a7f4-44ba-aab0-5c9ea76dc52b/dqc_reference/checkm_data
[2024-01-24 14:12:14,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:14,848] [INFO] Task started: CheckM
[2024-01-24 14:12:14,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/checkm_input GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:20,052] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:20,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:20,077] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:20,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:20,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:20,078] [INFO] Task started: Blastn
[2024-01-24 14:13:20,079] [INFO] Running command: blastn -query GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c4e76c8-a7f4-44ba-aab0-5c9ea76dc52b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:21,859] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:21,863] [INFO] Selected 16 target genomes.
[2024-01-24 14:13:21,863] [INFO] Target genome list was writen to GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:21,873] [INFO] Task started: fastANI
[2024-01-24 14:13:21,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cc0b11f-c079-4241-b91f-89bc6818016b/GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna.gz --refList GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:37,136] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:37,208] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:37,209] [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_900105205.1	s__Microbacterium hydrocarbonoxydans	100.0	1189	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001889265.1	s__Microbacterium sp001889265	86.3341	887	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.81	98.68	0.92	0.91	4	-
GCF_018613995.1	s__Microbacterium sp018613995	86.2858	669	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423615.1	s__Microbacterium sp001423615	86.1594	914	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.40	98.40	0.90	0.90	2	-
GCF_002024885.1	s__Microbacterium foliorum_A	86.1438	942	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	97.34	0.94	0.92	3	-
GCF_017876435.1	s__Microbacterium phyllosphaerae	86.0566	918	1193	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	86.0297	915	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385575.1	s__Microbacterium foliorum_B	85.9189	896	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426995.1	s__Microbacterium sp001426995	85.3461	875	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.85	97.85	0.92	0.92	2	-
GCF_003367705.1	s__Microbacterium foliorum	85.1497	865	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904831005.1	s__Microbacterium hydrocarbonoxydans_B	84.7272	858	1193	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	84.618	832	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355365.1	s__Microbacterium sp017355365	83.6609	739	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979415.1	s__Microbacterium sp002979415	83.4019	791	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967865.1	s__Microbacterium sp000967865	83.0617	761	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904066215.1	s__Microbacterium sp002456035	82.654	766	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	98.64	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:37,211] [INFO] GTDB search result was written to GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:37,211] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:37,217] [INFO] DFAST_QC result json was written to GCF_900105205.1_IMG-taxon_2634166363_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:37,217] [INFO] DFAST_QC completed!
[2024-01-24 14:13:37,217] [INFO] Total running time: 0h1m51s