[2024-01-24 13:52:11,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:11,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:11,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg93677fbe-7817-4281-83c9-8a76aa5278cb/dqc_reference
[2024-01-24 13:52:12,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:12,964] [INFO] Task started: Prodigal
[2024-01-24 13:52:12,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fcefa3d-6ba0-4ac1-a114-506a7e328dc3/GCF_003367705.1_ASM336770v1_genomic.fna.gz | prodigal -d GCF_003367705.1_ASM336770v1_genomic.fna/cds.fna -a GCF_003367705.1_ASM336770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:23,303] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:23,304] [INFO] Task started: HMMsearch
[2024-01-24 13:52:23,304] [INFO] Running command: hmmsearch --tblout GCF_003367705.1_ASM336770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93677fbe-7817-4281-83c9-8a76aa5278cb/dqc_reference/reference_markers.hmm GCF_003367705.1_ASM336770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:23,560] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:23,561] [INFO] Found 6/6 markers.
[2024-01-24 13:52:23,598] [INFO] Query marker FASTA was written to GCF_003367705.1_ASM336770v1_genomic.fna/markers.fasta
[2024-01-24 13:52:23,599] [INFO] Task started: Blastn
[2024-01-24 13:52:23,599] [INFO] Running command: blastn -query GCF_003367705.1_ASM336770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93677fbe-7817-4281-83c9-8a76aa5278cb/dqc_reference/reference_markers.fasta -out GCF_003367705.1_ASM336770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:24,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:24,735] [INFO] Selected 13 target genomes.
[2024-01-24 13:52:24,735] [INFO] Target genome list was writen to GCF_003367705.1_ASM336770v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:24,753] [INFO] Task started: fastANI
[2024-01-24 13:52:24,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fcefa3d-6ba0-4ac1-a114-506a7e328dc3/GCF_003367705.1_ASM336770v1_genomic.fna.gz --refList GCF_003367705.1_ASM336770v1_genomic.fna/target_genomes.txt --output GCF_003367705.1_ASM336770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:34,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:34,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93677fbe-7817-4281-83c9-8a76aa5278cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:34,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93677fbe-7817-4281-83c9-8a76aa5278cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:34,358] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:52:34,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:34,358] [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	100.0	1189	1189	95	conclusive
Microbacterium foliorum	strain=DSM 12966	GCA_000956415.1	104336	104336	suspected-type	True	99.9771	1154	1189	95	conclusive
Microbacterium phyllosphaerae	strain=DSM 13468	GCA_017876435.1	124798	124798	type	True	86.2072	890	1189	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	85.1535	828	1189	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	85.0479	877	1189	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	83.1333	780	1189	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	83.0207	715	1189	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	82.9675	721	1189	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.2579	573	1189	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.8093	511	1189	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.5644	508	1189	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.3286	469	1189	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.2961	463	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:34,360] [INFO] DFAST Taxonomy check result was written to GCF_003367705.1_ASM336770v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:34,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:34,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:34,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93677fbe-7817-4281-83c9-8a76aa5278cb/dqc_reference/checkm_data
[2024-01-24 13:52:34,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:34,401] [INFO] Task started: CheckM
[2024-01-24 13:52:34,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367705.1_ASM336770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367705.1_ASM336770v1_genomic.fna/checkm_input GCF_003367705.1_ASM336770v1_genomic.fna/checkm_result
[2024-01-24 13:53:37,841] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:37,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:37,864] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:37,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:37,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367705.1_ASM336770v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:37,865] [INFO] Task started: Blastn
[2024-01-24 13:53:37,866] [INFO] Running command: blastn -query GCF_003367705.1_ASM336770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93677fbe-7817-4281-83c9-8a76aa5278cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367705.1_ASM336770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:39,657] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:39,662] [INFO] Selected 13 target genomes.
[2024-01-24 13:53:39,662] [INFO] Target genome list was writen to GCF_003367705.1_ASM336770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:39,681] [INFO] Task started: fastANI
[2024-01-24 13:53:39,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fcefa3d-6ba0-4ac1-a114-506a7e328dc3/GCF_003367705.1_ASM336770v1_genomic.fna.gz --refList GCF_003367705.1_ASM336770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367705.1_ASM336770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:51,223] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:51,241] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:51,242] [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_003367705.1	s__Microbacterium foliorum	100.0	1189	1189	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_001426995.1	s__Microbacterium sp001426995	94.3226	1057	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.85	97.85	0.92	0.92	2	-
GCF_001423615.1	s__Microbacterium sp001423615	86.3213	905	1189	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	86.211	890	1189	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	86.1237	896	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613995.1	s__Microbacterium sp018613995	85.5657	637	1189	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	85.4271	891	1189	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	85.4228	868	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.81	98.68	0.92	0.91	4	-
GCF_006385575.1	s__Microbacterium foliorum_B	85.3068	884	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105205.1	s__Microbacterium hydrocarbonoxydans	85.0405	878	1189	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	84.4832	854	1189	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	84.3044	797	1189	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	83.3686	742	1189	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 13:53:51,245] [INFO] GTDB search result was written to GCF_003367705.1_ASM336770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:51,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:51,249] [INFO] DFAST_QC result json was written to GCF_003367705.1_ASM336770v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:51,249] [INFO] DFAST_QC completed!
[2024-01-24 13:53:51,249] [INFO] Total running time: 0h1m40s