[2024-01-24 13:49:40,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,056] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ba9cb26-ae03-48ce-8583-2cb1e1763a9f/dqc_reference
[2024-01-24 13:49:41,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,202] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,202] [INFO] Running command: gunzip -c /var/lib/cwl/stgd48927fc-dc98-42de-a34f-3417306e4d12/GCF_016907555.1_ASM1690755v1_genomic.fna.gz | prodigal -d GCF_016907555.1_ASM1690755v1_genomic.fna/cds.fna -a GCF_016907555.1_ASM1690755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,071] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,071] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,071] [INFO] Running command: hmmsearch --tblout GCF_016907555.1_ASM1690755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ba9cb26-ae03-48ce-8583-2cb1e1763a9f/dqc_reference/reference_markers.hmm GCF_016907555.1_ASM1690755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:49,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:49,255] [INFO] Found 6/6 markers.
[2024-01-24 13:49:49,279] [INFO] Query marker FASTA was written to GCF_016907555.1_ASM1690755v1_genomic.fna/markers.fasta
[2024-01-24 13:49:49,279] [INFO] Task started: Blastn
[2024-01-24 13:49:49,279] [INFO] Running command: blastn -query GCF_016907555.1_ASM1690755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba9cb26-ae03-48ce-8583-2cb1e1763a9f/dqc_reference/reference_markers.fasta -out GCF_016907555.1_ASM1690755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,349] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,351] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:50,352] [INFO] Target genome list was writen to GCF_016907555.1_ASM1690755v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,356] [INFO] Task started: fastANI
[2024-01-24 13:49:50,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgd48927fc-dc98-42de-a34f-3417306e4d12/GCF_016907555.1_ASM1690755v1_genomic.fna.gz --refList GCF_016907555.1_ASM1690755v1_genomic.fna/target_genomes.txt --output GCF_016907555.1_ASM1690755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:00,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ba9cb26-ae03-48ce-8583-2cb1e1763a9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:00,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ba9cb26-ae03-48ce-8583-2cb1e1763a9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:00,618] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:00,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:00,618] [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 laevaniformans	strain=DSM 20140	GCA_016907555.1	36807	36807	type	True	100.0	1008	1010	95	conclusive
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	85.9196	739	1010	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	85.8855	753	1010	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	83.2092	659	1010	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	82.6584	619	1010	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	82.6127	584	1010	95	below_threshold
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	82.6031	591	1010	95	below_threshold
Microbacterium paulum	strain=2C	GCA_015707995.1	2707006	2707006	type	True	82.585	602	1010	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	82.1855	603	1010	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.6547	587	1010	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.6937	499	1010	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	80.6778	502	1010	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.28	499	1010	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.2097	486	1010	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.1797	505	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,620] [INFO] DFAST Taxonomy check result was written to GCF_016907555.1_ASM1690755v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:00,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:00,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:00,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ba9cb26-ae03-48ce-8583-2cb1e1763a9f/dqc_reference/checkm_data
[2024-01-24 13:50:00,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:00,650] [INFO] Task started: CheckM
[2024-01-24 13:50:00,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907555.1_ASM1690755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907555.1_ASM1690755v1_genomic.fna/checkm_input GCF_016907555.1_ASM1690755v1_genomic.fna/checkm_result
[2024-01-24 13:50:49,861] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:49,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:49,883] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:49,883] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:49,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907555.1_ASM1690755v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:49,884] [INFO] Task started: Blastn
[2024-01-24 13:50:49,884] [INFO] Running command: blastn -query GCF_016907555.1_ASM1690755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba9cb26-ae03-48ce-8583-2cb1e1763a9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907555.1_ASM1690755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:51,676] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:51,679] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:51,679] [INFO] Target genome list was writen to GCF_016907555.1_ASM1690755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:51,687] [INFO] Task started: fastANI
[2024-01-24 13:50:51,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgd48927fc-dc98-42de-a34f-3417306e4d12/GCF_016907555.1_ASM1690755v1_genomic.fna.gz --refList GCF_016907555.1_ASM1690755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907555.1_ASM1690755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:58,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:58,355] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:58,356] [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_016907555.1	s__Microbacterium laevaniformans	100.0	1009	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.33	96.04	0.85	0.81	5	conclusive
GCF_000411455.1	s__Microbacterium sp000411455	94.3208	823	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.03	96.01	0.82	0.82	3	-
GCF_003293595.1	s__Microbacterium sp003293595	93.8334	817	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.08	97.59	0.90	0.89	4	-
GCF_001592125.1	s__Microbacterium hominis	85.8855	753	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.42	0.92	0.89	6	-
GCF_015350795.1	s__Microbacterium sp015350795	83.9198	727	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907815.1	s__Microbacterium aurum	83.2352	657	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	-
GCA_001898315.1	s__Microbacterium sp001898315	82.2834	602	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_003651225.1	s__Microbacterium telephonicum	81.6545	587	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828185.1	s__Microbacterium sp007828185	80.9507	527	1010	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 13:50:58,357] [INFO] GTDB search result was written to GCF_016907555.1_ASM1690755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:58,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:58,360] [INFO] DFAST_QC result json was written to GCF_016907555.1_ASM1690755v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:58,360] [INFO] DFAST_QC completed!
[2024-01-24 13:50:58,361] [INFO] Total running time: 0h1m18s