[2023-03-18 22:22:21,945] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:22:21,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:22:21,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b28c6b2-9e84-4a5b-93fc-eaced62d16f7/dqc_reference
[2023-03-18 22:22:23,029] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:22:23,029] [INFO] Task started: Prodigal
[2023-03-18 22:22:23,029] [INFO] Running command: cat /var/lib/cwl/stg46ef9c27-670f-403e-8e0f-c3a20da274b4/OceanDNA-b2641.fa | prodigal -d OceanDNA-b2641/cds.fna -a OceanDNA-b2641/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:22:36,192] [INFO] Task succeeded: Prodigal
[2023-03-18 22:22:36,192] [INFO] Task started: HMMsearch
[2023-03-18 22:22:36,192] [INFO] Running command: hmmsearch --tblout OceanDNA-b2641/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b28c6b2-9e84-4a5b-93fc-eaced62d16f7/dqc_reference/reference_markers.hmm OceanDNA-b2641/protein.faa > /dev/null
[2023-03-18 22:22:36,375] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:22:36,375] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg46ef9c27-670f-403e-8e0f-c3a20da274b4/OceanDNA-b2641.fa]
[2023-03-18 22:22:36,392] [INFO] Query marker FASTA was written to OceanDNA-b2641/markers.fasta
[2023-03-18 22:22:36,393] [INFO] Task started: Blastn
[2023-03-18 22:22:36,393] [INFO] Running command: blastn -query OceanDNA-b2641/markers.fasta -db /var/lib/cwl/stg3b28c6b2-9e84-4a5b-93fc-eaced62d16f7/dqc_reference/reference_markers.fasta -out OceanDNA-b2641/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:22:37,690] [INFO] Task succeeded: Blastn
[2023-03-18 22:22:37,691] [INFO] Selected 19 target genomes.
[2023-03-18 22:22:37,691] [INFO] Target genome list was writen to OceanDNA-b2641/target_genomes.txt
[2023-03-18 22:22:37,703] [INFO] Task started: fastANI
[2023-03-18 22:22:37,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ef9c27-670f-403e-8e0f-c3a20da274b4/OceanDNA-b2641.fa --refList OceanDNA-b2641/target_genomes.txt --output OceanDNA-b2641/fastani_result.tsv --threads 1
[2023-03-18 22:22:49,781] [INFO] Task succeeded: fastANI
[2023-03-18 22:22:49,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b28c6b2-9e84-4a5b-93fc-eaced62d16f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:22:49,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b28c6b2-9e84-4a5b-93fc-eaced62d16f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:22:49,842] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 22:22:49,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 22:22:49,842] [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 marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	96.2065	632	728	95	conclusive
Microbacterium oleivorans	strain=NBRC 103075	GCA_001552475.1	273677	273677	suspected-type	True	82.576	486	728	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.3293	423	728	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.1824	432	728	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	81.1654	410	728	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.1074	428	728	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	80.9708	395	728	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.8703	410	728	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.6119	384	728	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.5195	414	728	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.4714	379	728	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	80.3982	391	728	95	below_threshold
Microbacterium laevaniformans	strain=DSM 20140	GCA_016907555.1	36807	36807	type	True	80.2465	370	728	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	80.2113	400	728	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.198	379	728	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.1386	391	728	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.1046	373	728	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.0696	387	728	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.0194	370	728	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:22:49,843] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2641/tc_result.tsv
[2023-03-18 22:22:49,843] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:22:49,843] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:22:49,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b28c6b2-9e84-4a5b-93fc-eaced62d16f7/dqc_reference/checkm_data
[2023-03-18 22:22:49,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:22:49,847] [INFO] Task started: CheckM
[2023-03-18 22:22:49,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2641/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2641/checkm_input OceanDNA-b2641/checkm_result
[2023-03-18 22:23:33,792] [INFO] Task succeeded: CheckM
[2023-03-18 22:23:33,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:23:33,795] [INFO] ===== Completeness check finished =====
[2023-03-18 22:23:33,795] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:23:33,795] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2641/markers.fasta)
[2023-03-18 22:23:33,797] [INFO] Task started: Blastn
[2023-03-18 22:23:33,797] [INFO] Running command: blastn -query OceanDNA-b2641/markers.fasta -db /var/lib/cwl/stg3b28c6b2-9e84-4a5b-93fc-eaced62d16f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2641/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:23:36,081] [INFO] Task succeeded: Blastn
[2023-03-18 22:23:36,082] [INFO] Selected 8 target genomes.
[2023-03-18 22:23:36,082] [INFO] Target genome list was writen to OceanDNA-b2641/target_genomes_gtdb.txt
[2023-03-18 22:23:36,092] [INFO] Task started: fastANI
[2023-03-18 22:23:36,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ef9c27-670f-403e-8e0f-c3a20da274b4/OceanDNA-b2641.fa --refList OceanDNA-b2641/target_genomes_gtdb.txt --output OceanDNA-b2641/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:23:41,105] [INFO] Task succeeded: fastANI
[2023-03-18 22:23:41,111] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:23:41,111] [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_014204835.1	s__Microbacterium marinum	96.2065	632	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.15	96.15	0.88	0.88	2	conclusive
GCF_001644225.1	s__Microbacterium oleivorans_A	83.4285	515	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102005.1	s__Microbacterium sp900102005	82.9548	489	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.39	98.39	0.95	0.95	2	-
GCF_000383475.1	s__Microbacterium sp000383475	82.9472	499	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.27	98.25	0.96	0.95	4	-
GCF_001691565.1	s__Microbacterium oleivorans_B	82.9289	489	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552475.1	s__Microbacterium oleivorans	82.5821	486	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.13	99.05	0.96	0.96	4	-
GCF_015278255.1	s__Microbacterium hibisci	80.6225	383	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282805.1	s__Microbacterium hominis_B	80.1421	387	728	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 22:23:41,111] [INFO] GTDB search result was written to OceanDNA-b2641/result_gtdb.tsv
[2023-03-18 22:23:41,111] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:23:41,113] [INFO] DFAST_QC result json was written to OceanDNA-b2641/dqc_result.json
[2023-03-18 22:23:41,113] [INFO] DFAST_QC completed!
[2023-03-18 22:23:41,113] [INFO] Total running time: 0h1m19s