[2023-03-18 01:43:48,633] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:43:48,633] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:43:48,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg98c0d0f3-777d-453e-b316-0bdf64fbf782/dqc_reference
[2023-03-18 01:43:49,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:43:49,745] [INFO] Task started: Prodigal
[2023-03-18 01:43:49,745] [INFO] Running command: cat /var/lib/cwl/stg7b6f31a3-55db-4b6f-a247-3552d7dd8519/OceanDNA-b2589.fa | prodigal -d OceanDNA-b2589/cds.fna -a OceanDNA-b2589/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:43:59,095] [INFO] Task succeeded: Prodigal
[2023-03-18 01:43:59,095] [INFO] Task started: HMMsearch
[2023-03-18 01:43:59,095] [INFO] Running command: hmmsearch --tblout OceanDNA-b2589/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98c0d0f3-777d-453e-b316-0bdf64fbf782/dqc_reference/reference_markers.hmm OceanDNA-b2589/protein.faa > /dev/null
[2023-03-18 01:43:59,241] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:43:59,241] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7b6f31a3-55db-4b6f-a247-3552d7dd8519/OceanDNA-b2589.fa]
[2023-03-18 01:43:59,252] [INFO] Query marker FASTA was written to OceanDNA-b2589/markers.fasta
[2023-03-18 01:43:59,254] [INFO] Task started: Blastn
[2023-03-18 01:43:59,254] [INFO] Running command: blastn -query OceanDNA-b2589/markers.fasta -db /var/lib/cwl/stg98c0d0f3-777d-453e-b316-0bdf64fbf782/dqc_reference/reference_markers.fasta -out OceanDNA-b2589/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:00,417] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:00,418] [INFO] Selected 23 target genomes.
[2023-03-18 01:44:00,418] [INFO] Target genome list was writen to OceanDNA-b2589/target_genomes.txt
[2023-03-18 01:44:00,427] [INFO] Task started: fastANI
[2023-03-18 01:44:00,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6f31a3-55db-4b6f-a247-3552d7dd8519/OceanDNA-b2589.fa --refList OceanDNA-b2589/target_genomes.txt --output OceanDNA-b2589/fastani_result.tsv --threads 1
[2023-03-18 01:44:13,570] [INFO] Task succeeded: fastANI
[2023-03-18 01:44:13,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98c0d0f3-777d-453e-b316-0bdf64fbf782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:44:13,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98c0d0f3-777d-453e-b316-0bdf64fbf782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:44:13,584] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 01:44:13,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:44:13,584] [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 ginsengisoli	strain=DSM 18659	GCA_000956535.1	400772	400772	type	True	99.6631	487	517	95	conclusive
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	81.2941	329	517	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	81.248	328	517	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.1458	316	517	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	81.0713	339	517	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	81.0275	304	517	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.0272	320	517	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.9699	329	517	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	80.9508	317	517	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	80.9398	310	517	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.9204	327	517	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	80.8999	333	517	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.8106	327	517	95	below_threshold
Microbacterium mangrovi	strain=MUSC 115	GCA_000802305.1	1348253	1348253	type	True	80.7878	302	517	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.7454	330	517	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	80.6192	309	517	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	80.5252	324	517	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	80.503	268	517	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	80.4828	330	517	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	80.4819	268	517	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	80.4681	269	517	95	below_threshold
Microbacterium caowuchunii	strain=ST-M6	GCA_008727755.1	2614638	2614638	type	True	80.4256	284	517	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	80.3824	297	517	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:44:13,584] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2589/tc_result.tsv
[2023-03-18 01:44:13,584] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:44:13,584] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:44:13,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98c0d0f3-777d-453e-b316-0bdf64fbf782/dqc_reference/checkm_data
[2023-03-18 01:44:13,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:44:13,588] [INFO] Task started: CheckM
[2023-03-18 01:44:13,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2589/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2589/checkm_input OceanDNA-b2589/checkm_result
[2023-03-18 01:44:45,865] [INFO] Task succeeded: CheckM
[2023-03-18 01:44:45,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:44:45,868] [INFO] ===== Completeness check finished =====
[2023-03-18 01:44:45,868] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:44:45,868] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2589/markers.fasta)
[2023-03-18 01:44:45,869] [INFO] Task started: Blastn
[2023-03-18 01:44:45,869] [INFO] Running command: blastn -query OceanDNA-b2589/markers.fasta -db /var/lib/cwl/stg98c0d0f3-777d-453e-b316-0bdf64fbf782/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2589/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:47,836] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:47,837] [INFO] Selected 24 target genomes.
[2023-03-18 01:44:47,837] [INFO] Target genome list was writen to OceanDNA-b2589/target_genomes_gtdb.txt
[2023-03-18 01:44:47,852] [INFO] Task started: fastANI
[2023-03-18 01:44:47,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6f31a3-55db-4b6f-a247-3552d7dd8519/OceanDNA-b2589.fa --refList OceanDNA-b2589/target_genomes_gtdb.txt --output OceanDNA-b2589/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:45:03,119] [INFO] Task succeeded: fastANI
[2023-03-18 01:45:03,132] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:45:03,132] [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_000956535.1	s__Microbacterium ginsengisoli	99.6631	487	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.60	98.14	0.85	0.83	9	conclusive
GCF_003651225.1	s__Microbacterium telephonicum	81.5095	320	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	81.2921	329	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706225.1	s__Microbacterium sp902706225	81.2544	318	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931875.1	s__Microbacterium sp003931875	81.2485	337	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	81.23	337	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	81.2265	329	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716815.1	s__Microbacterium lacticum	81.2011	327	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCF_001314225.1	s__Microbacterium sp001314225	81.1963	332	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	81.0904	338	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	81.0672	350	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	80.986	234	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759705.1	s__Microbacterium ulmi	80.9747	308	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000799385.1	s__Microbacterium sp000799385	80.8854	325	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802305.1	s__Microbacterium mangrovi	80.7666	303	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715675.1	s__Microbacterium sp006715675	80.6877	335	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046485.1	s__Microbacterium sp011046485	80.6681	328	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422405.1	s__Microbacterium luticocti	80.6198	309	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362195.1	s__Microbacterium sp004362195	80.5927	314	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564075.1	s__Microbacterium sediminis	80.4971	268	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_008727755.1	s__Microbacterium caowuchunii	80.3784	287	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.11	97.11	0.88	0.88	2	-
GCF_004564355.1	s__Microbacterium wangchenii	80.3625	298	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.29	98.90	0.96	0.95	3	-
GCF_009649635.1	s__Microbacterium sp009649635	80.092	280	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014171575.1	s__Microbacterium sp014171575	79.7016	265	517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:45:03,133] [INFO] GTDB search result was written to OceanDNA-b2589/result_gtdb.tsv
[2023-03-18 01:45:03,133] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:45:03,135] [INFO] DFAST_QC result json was written to OceanDNA-b2589/dqc_result.json
[2023-03-18 01:45:03,135] [INFO] DFAST_QC completed!
[2023-03-18 01:45:03,135] [INFO] Total running time: 0h1m15s