[2023-03-15 17:24:01,306] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,308] [INFO] DQC Reference Directory: /var/lib/cwl/stgdffbd5a6-54a9-4458-9a84-bb9df26c35ef/dqc_reference
[2023-03-15 17:24:02,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,579] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,580] [INFO] Running command: cat /var/lib/cwl/stg64053398-e052-41af-854a-10048b76a8c5/OceanDNA-b2647.fa | prodigal -d OceanDNA-b2647/cds.fna -a OceanDNA-b2647/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:23,096] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:23,097] [INFO] Task started: HMMsearch
[2023-03-15 17:24:23,097] [INFO] Running command: hmmsearch --tblout OceanDNA-b2647/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdffbd5a6-54a9-4458-9a84-bb9df26c35ef/dqc_reference/reference_markers.hmm OceanDNA-b2647/protein.faa > /dev/null
[2023-03-15 17:24:23,311] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:23,311] [INFO] Found 6/6 markers.
[2023-03-15 17:24:23,332] [INFO] Query marker FASTA was written to OceanDNA-b2647/markers.fasta
[2023-03-15 17:24:23,333] [INFO] Task started: Blastn
[2023-03-15 17:24:23,333] [INFO] Running command: blastn -query OceanDNA-b2647/markers.fasta -db /var/lib/cwl/stgdffbd5a6-54a9-4458-9a84-bb9df26c35ef/dqc_reference/reference_markers.fasta -out OceanDNA-b2647/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:24,469] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:24,470] [INFO] Selected 19 target genomes.
[2023-03-15 17:24:24,470] [INFO] Target genome list was writen to OceanDNA-b2647/target_genomes.txt
[2023-03-15 17:24:24,482] [INFO] Task started: fastANI
[2023-03-15 17:24:24,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg64053398-e052-41af-854a-10048b76a8c5/OceanDNA-b2647.fa --refList OceanDNA-b2647/target_genomes.txt --output OceanDNA-b2647/fastani_result.tsv --threads 1
[2023-03-15 17:24:38,705] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:38,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdffbd5a6-54a9-4458-9a84-bb9df26c35ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:38,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdffbd5a6-54a9-4458-9a84-bb9df26c35ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:38,717] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 17:24:38,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 17:24:38,717] [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 luteum	strain=A18JL200	GCA_015277875.1	2782167	2782167	type	True	97.7006	937	1090	95	conclusive
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	80.5188	551	1090	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.4657	531	1090	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.179	533	1090	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.155	558	1090	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.1203	554	1090	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.1192	512	1090	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.1051	495	1090	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.0929	548	1090	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.0669	512	1090	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	79.8828	497	1090	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	79.8488	492	1090	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.831	536	1090	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	79.7695	490	1090	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	79.7384	515	1090	95	below_threshold
Microbacterium ginsengisoli	strain=DSM 18659	GCA_000956535.1	400772	400772	type	True	79.6778	455	1090	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	79.3936	439	1090	95	below_threshold
Microbacterium profundi	strain=Shh49	GCA_000763375.1	450380	450380	type	True	79.3145	378	1090	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	79.156	378	1090	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:24:38,717] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2647/tc_result.tsv
[2023-03-15 17:24:38,717] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:38,717] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:38,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdffbd5a6-54a9-4458-9a84-bb9df26c35ef/dqc_reference/checkm_data
[2023-03-15 17:24:38,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:38,723] [INFO] Task started: CheckM
[2023-03-15 17:24:38,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2647/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2647/checkm_input OceanDNA-b2647/checkm_result
[2023-03-15 17:25:39,603] [INFO] Task succeeded: CheckM
[2023-03-15 17:25:39,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:25:39,606] [INFO] ===== Completeness check finished =====
[2023-03-15 17:25:39,606] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:25:39,606] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2647/markers.fasta)
[2023-03-15 17:25:39,607] [INFO] Task started: Blastn
[2023-03-15 17:25:39,607] [INFO] Running command: blastn -query OceanDNA-b2647/markers.fasta -db /var/lib/cwl/stgdffbd5a6-54a9-4458-9a84-bb9df26c35ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2647/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:41,270] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:41,271] [INFO] Selected 21 target genomes.
[2023-03-15 17:25:41,271] [INFO] Target genome list was writen to OceanDNA-b2647/target_genomes_gtdb.txt
[2023-03-15 17:25:41,296] [INFO] Task started: fastANI
[2023-03-15 17:25:41,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg64053398-e052-41af-854a-10048b76a8c5/OceanDNA-b2647.fa --refList OceanDNA-b2647/target_genomes_gtdb.txt --output OceanDNA-b2647/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:25:56,285] [INFO] Task succeeded: fastANI
[2023-03-15 17:25:56,296] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:25:56,297] [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_015277875.1	s__Microbacterium sp900098805	97.6783	938	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.54	97.00	0.83	0.71	9	conclusive
GCA_002703245.1	s__Microbacterium sp002703245	83.0611	601	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	80.4767	530	1090	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	80.222	538	1090	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	80.1856	555	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	80.1792	533	1090	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	80.1716	549	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837165.1	s__Microbacterium sp014837165	80.1566	509	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	80.1091	495	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	80.0963	559	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003999995.1	s__Microbacterium sp003999995	80.0893	510	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858275.1	s__Microbacterium sp009858275	80.0545	546	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012847295.1	s__Microbacterium sp012847295	80.0385	496	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900155915.1	s__Microbacterium sp900155915	79.931	486	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836535.1	s__Microbacterium sp014836535	79.8379	493	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017415.1	s__Microbacterium hatanonis	79.7587	491	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799385.1	s__Microbacterium sp000799385	79.7501	482	1090	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	79.7372	471	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900292075.1	s__Microbacterium timonense	79.7339	516	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870695.1	s__Microbacterium sp016870695	79.5783	347	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552355.1	s__Microbacterium resistens	79.1365	379	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:25:56,297] [INFO] GTDB search result was written to OceanDNA-b2647/result_gtdb.tsv
[2023-03-15 17:25:56,297] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:25:56,299] [INFO] DFAST_QC result json was written to OceanDNA-b2647/dqc_result.json
[2023-03-15 17:25:56,299] [INFO] DFAST_QC completed!
[2023-03-15 17:25:56,299] [INFO] Total running time: 0h1m55s