[2024-01-24 13:21:11,184] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,187] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg8db6d806-1cb6-4fda-8bb5-d77e2c5186a2/dqc_reference
[2024-01-24 13:21:12,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,363] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgda6261cd-ae11-4fef-a78d-e76e274aa226/GCF_014635005.1_ASM1463500v1_genomic.fna.gz | prodigal -d GCF_014635005.1_ASM1463500v1_genomic.fna/cds.fna -a GCF_014635005.1_ASM1463500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:21,812] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:21,813] [INFO] Task started: HMMsearch
[2024-01-24 13:21:21,813] [INFO] Running command: hmmsearch --tblout GCF_014635005.1_ASM1463500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8db6d806-1cb6-4fda-8bb5-d77e2c5186a2/dqc_reference/reference_markers.hmm GCF_014635005.1_ASM1463500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:22,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:22,064] [INFO] Found 6/6 markers.
[2024-01-24 13:21:22,093] [INFO] Query marker FASTA was written to GCF_014635005.1_ASM1463500v1_genomic.fna/markers.fasta
[2024-01-24 13:21:22,094] [INFO] Task started: Blastn
[2024-01-24 13:21:22,094] [INFO] Running command: blastn -query GCF_014635005.1_ASM1463500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8db6d806-1cb6-4fda-8bb5-d77e2c5186a2/dqc_reference/reference_markers.fasta -out GCF_014635005.1_ASM1463500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:23,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:23,292] [INFO] Selected 15 target genomes.
[2024-01-24 13:21:23,292] [INFO] Target genome list was writen to GCF_014635005.1_ASM1463500v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:23,305] [INFO] Task started: fastANI
[2024-01-24 13:21:23,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgda6261cd-ae11-4fef-a78d-e76e274aa226/GCF_014635005.1_ASM1463500v1_genomic.fna.gz --refList GCF_014635005.1_ASM1463500v1_genomic.fna/target_genomes.txt --output GCF_014635005.1_ASM1463500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:34,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:34,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8db6d806-1cb6-4fda-8bb5-d77e2c5186a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:34,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8db6d806-1cb6-4fda-8bb5-d77e2c5186a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:34,405] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:21:34,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:34,405] [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 aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	100.0	1076	1076	95	conclusive
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	99.9898	1056	1076	95	conclusive
Microbacterium ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	83.8617	692	1076	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	83.8606	699	1076	95	below_threshold
Microbacterium profundi	strain=Shh49	GCA_000763375.1	450380	450380	type	True	83.3873	725	1076	95	below_threshold
Microbacterium murale	strain=CCM 7640	GCA_014635185.1	1081040	1081040	type	True	83.2335	785	1076	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	81.8795	611	1076	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	81.8399	614	1076	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.7249	554	1076	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	81.646	608	1076	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.6078	580	1076	95	below_threshold
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	81.1404	552	1076	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.1172	461	1076	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.8818	493	1076	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.6741	469	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:34,406] [INFO] DFAST Taxonomy check result was written to GCF_014635005.1_ASM1463500v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:34,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:34,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:34,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8db6d806-1cb6-4fda-8bb5-d77e2c5186a2/dqc_reference/checkm_data
[2024-01-24 13:21:34,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:34,440] [INFO] Task started: CheckM
[2024-01-24 13:21:34,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635005.1_ASM1463500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635005.1_ASM1463500v1_genomic.fna/checkm_input GCF_014635005.1_ASM1463500v1_genomic.fna/checkm_result
[2024-01-24 13:22:23,209] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:23,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:23,228] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:23,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:23,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635005.1_ASM1463500v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:23,230] [INFO] Task started: Blastn
[2024-01-24 13:22:23,230] [INFO] Running command: blastn -query GCF_014635005.1_ASM1463500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8db6d806-1cb6-4fda-8bb5-d77e2c5186a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635005.1_ASM1463500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:25,328] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:25,332] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:25,332] [INFO] Target genome list was writen to GCF_014635005.1_ASM1463500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:25,341] [INFO] Task started: fastANI
[2024-01-24 13:22:25,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgda6261cd-ae11-4fef-a78d-e76e274aa226/GCF_014635005.1_ASM1463500v1_genomic.fna.gz --refList GCF_014635005.1_ASM1463500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635005.1_ASM1463500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:36,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:36,167] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:36,167] [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_007988825.1	s__Microbacterium aerolatum	99.9898	1056	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_015277895.1	s__Microbacterium sp015277895	89.607	857	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645325.1	s__Microbacterium sp903645325	85.0221	682	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205075.1	s__Microbacterium ginsengiterrae	83.8514	693	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.21	98.43	0.95	0.89	3	-
GCF_000763375.1	s__Microbacterium profundi	83.3963	724	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.00	98.00	0.85	0.85	2	-
GCF_014635185.1	s__Microbacterium murale	83.2416	784	1076	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	82.2002	607	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.61	99.21	0.98	0.97	3	-
GCF_900105205.1	s__Microbacterium hydrocarbonoxydans	81.8518	613	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002979415.1	s__Microbacterium sp002979415	81.8	613	1076	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	81.6199	579	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872075.1	s__Microbacterium kitamiense	81.4139	615	1076	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	80.857	532	1076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_006783905.1	s__Microbacterium kyungheense	80.0673	505	1076	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 13:22:36,171] [INFO] GTDB search result was written to GCF_014635005.1_ASM1463500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:36,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:36,175] [INFO] DFAST_QC result json was written to GCF_014635005.1_ASM1463500v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:36,176] [INFO] DFAST_QC completed!
[2024-01-24 13:22:36,176] [INFO] Total running time: 0h1m25s