[2024-01-24 11:26:54,313] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,320] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,320] [INFO] DQC Reference Directory: /var/lib/cwl/stge22a8b04-7fa9-4261-b4ab-eb986f816a8f/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,223] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eed735c-5e0e-4381-a915-afa5d344ba2c/GCF_016907815.1_ASM1690781v1_genomic.fna.gz | prodigal -d GCF_016907815.1_ASM1690781v1_genomic.fna/cds.fna -a GCF_016907815.1_ASM1690781v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:08,341] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:08,341] [INFO] Task started: HMMsearch
[2024-01-24 11:27:08,341] [INFO] Running command: hmmsearch --tblout GCF_016907815.1_ASM1690781v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge22a8b04-7fa9-4261-b4ab-eb986f816a8f/dqc_reference/reference_markers.hmm GCF_016907815.1_ASM1690781v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:08,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:08,606] [INFO] Found 6/6 markers.
[2024-01-24 11:27:08,640] [INFO] Query marker FASTA was written to GCF_016907815.1_ASM1690781v1_genomic.fna/markers.fasta
[2024-01-24 11:27:08,641] [INFO] Task started: Blastn
[2024-01-24 11:27:08,641] [INFO] Running command: blastn -query GCF_016907815.1_ASM1690781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge22a8b04-7fa9-4261-b4ab-eb986f816a8f/dqc_reference/reference_markers.fasta -out GCF_016907815.1_ASM1690781v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,999] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:10,003] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:10,003] [INFO] Target genome list was writen to GCF_016907815.1_ASM1690781v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:10,005] [INFO] Task started: fastANI
[2024-01-24 11:27:10,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eed735c-5e0e-4381-a915-afa5d344ba2c/GCF_016907815.1_ASM1690781v1_genomic.fna.gz --refList GCF_016907815.1_ASM1690781v1_genomic.fna/target_genomes.txt --output GCF_016907815.1_ASM1690781v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:21,749] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:21,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge22a8b04-7fa9-4261-b4ab-eb986f816a8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:21,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge22a8b04-7fa9-4261-b4ab-eb986f816a8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:21,763] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:21,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:21,764] [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 aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	100.0	1137	1137	95	conclusive
Microbacterium lacticum	strain=DSM 20427	GCA_006716815.1	33885	33885	type	True	84.3442	673	1137	95	below_threshold
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	84.2823	642	1137	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	84.2435	652	1137	95	below_threshold
Microbacterium paulum	strain=2C	GCA_015707995.1	2707006	2707006	type	True	83.9487	649	1137	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	83.8981	660	1137	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	83.8409	653	1137	95	below_threshold
Microbacterium laevaniformans	strain=DSM 20140	GCA_016907555.1	36807	36807	type	True	83.0889	659	1137	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	82.8118	635	1137	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	82.8086	645	1137	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	82.7958	658	1137	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	81.6128	581	1137	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	81.5711	579	1137	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	81.2569	585	1137	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.2077	557	1137	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.743	576	1137	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,766] [INFO] DFAST Taxonomy check result was written to GCF_016907815.1_ASM1690781v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:21,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:21,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:21,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge22a8b04-7fa9-4261-b4ab-eb986f816a8f/dqc_reference/checkm_data
[2024-01-24 11:27:21,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:21,873] [INFO] Task started: CheckM
[2024-01-24 11:27:21,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907815.1_ASM1690781v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907815.1_ASM1690781v1_genomic.fna/checkm_input GCF_016907815.1_ASM1690781v1_genomic.fna/checkm_result
[2024-01-24 11:28:17,774] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:17,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:17,798] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:17,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:17,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907815.1_ASM1690781v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:17,800] [INFO] Task started: Blastn
[2024-01-24 11:28:17,800] [INFO] Running command: blastn -query GCF_016907815.1_ASM1690781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge22a8b04-7fa9-4261-b4ab-eb986f816a8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907815.1_ASM1690781v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:20,216] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:20,222] [INFO] Selected 16 target genomes.
[2024-01-24 11:28:20,222] [INFO] Target genome list was writen to GCF_016907815.1_ASM1690781v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:20,229] [INFO] Task started: fastANI
[2024-01-24 11:28:20,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eed735c-5e0e-4381-a915-afa5d344ba2c/GCF_016907815.1_ASM1690781v1_genomic.fna.gz --refList GCF_016907815.1_ASM1690781v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907815.1_ASM1690781v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:31,654] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:31,674] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:31,674] [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_016907815.1	s__Microbacterium aurum	100.0	1137	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	conclusive
GCF_006716815.1	s__Microbacterium lacticum	84.2696	675	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCA_001898315.1	s__Microbacterium sp001898315	84.2258	678	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_015707995.1	s__Microbacterium sp015707995	83.9693	648	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592125.1	s__Microbacterium hominis	83.8526	652	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.42	0.92	0.89	6	-
GCA_017305435.1	s__Microbacterium sp017305435	83.6331	655	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248655.1	s__Microbacterium sp003248655	83.5077	637	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016807485.1	s__Microbacterium sp016807485	83.1014	410	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907555.1	s__Microbacterium laevaniformans	83.1014	660	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.33	96.04	0.85	0.81	5	-
GCF_016907295.1	s__Microbacterium dextranolyticum	82.857	631	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293595.1	s__Microbacterium sp003293595	82.8515	616	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.08	97.59	0.90	0.89	4	-
GCF_003651225.1	s__Microbacterium telephonicum	82.8209	644	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018717645.1	s__Microbacterium flavum	82.7958	658	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724425.1	s__Microbacterium sp001724425	82.768	610	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_003248845.1	s__Microbacterium sp003248845	82.6611	433	1137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCF_007828185.1	s__Microbacterium sp007828185	81.8097	593	1137	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 11:28:31,675] [INFO] GTDB search result was written to GCF_016907815.1_ASM1690781v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:31,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:31,682] [INFO] DFAST_QC result json was written to GCF_016907815.1_ASM1690781v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:31,683] [INFO] DFAST_QC completed!
[2024-01-24 11:28:31,683] [INFO] Total running time: 0h1m37s