[2023-03-17 07:28:31,295] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,295] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg66b127ad-4c4d-4865-8af0-8c474f70b089/dqc_reference
[2023-03-17 07:28:33,080] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,081] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,081] [INFO] Running command: cat /var/lib/cwl/stgd620f71b-7d51-427d-8825-e821bf638ed3/OceanDNA-b2630.fa | prodigal -d OceanDNA-b2630/cds.fna -a OceanDNA-b2630/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:52,752] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:52,752] [INFO] Task started: HMMsearch
[2023-03-17 07:28:52,752] [INFO] Running command: hmmsearch --tblout OceanDNA-b2630/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66b127ad-4c4d-4865-8af0-8c474f70b089/dqc_reference/reference_markers.hmm OceanDNA-b2630/protein.faa > /dev/null
[2023-03-17 07:28:52,973] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:52,974] [INFO] Found 6/6 markers.
[2023-03-17 07:28:52,993] [INFO] Query marker FASTA was written to OceanDNA-b2630/markers.fasta
[2023-03-17 07:28:52,993] [INFO] Task started: Blastn
[2023-03-17 07:28:52,993] [INFO] Running command: blastn -query OceanDNA-b2630/markers.fasta -db /var/lib/cwl/stg66b127ad-4c4d-4865-8af0-8c474f70b089/dqc_reference/reference_markers.fasta -out OceanDNA-b2630/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:54,011] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:54,012] [INFO] Selected 30 target genomes.
[2023-03-17 07:28:54,013] [INFO] Target genome list was writen to OceanDNA-b2630/target_genomes.txt
[2023-03-17 07:28:54,030] [INFO] Task started: fastANI
[2023-03-17 07:28:54,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgd620f71b-7d51-427d-8825-e821bf638ed3/OceanDNA-b2630.fa --refList OceanDNA-b2630/target_genomes.txt --output OceanDNA-b2630/fastani_result.tsv --threads 1
[2023-03-17 07:29:13,226] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:13,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66b127ad-4c4d-4865-8af0-8c474f70b089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:29:13,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66b127ad-4c4d-4865-8af0-8c474f70b089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:29:13,242] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:29:13,242] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:29:13,243] [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 thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	79.9092	450	1042	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	79.8419	400	1042	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	79.7847	391	1042	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	79.716	416	1042	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	79.7012	424	1042	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	79.7004	431	1042	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.661	401	1042	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	79.5841	392	1042	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	79.5714	401	1042	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	79.4969	399	1042	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	79.4683	401	1042	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	79.4567	419	1042	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	79.4339	412	1042	95	below_threshold
Microbacterium caowuchunii	strain=ST-M6	GCA_008727755.1	2614638	2614638	type	True	79.4301	348	1042	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.4221	429	1042	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.3629	421	1042	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	79.351	431	1042	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	79.3067	407	1042	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	79.286	383	1042	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	79.2645	361	1042	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.2623	392	1042	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.2548	392	1042	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.2545	420	1042	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	79.2532	359	1042	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	79.2519	374	1042	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	79.2311	357	1042	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	78.9848	329	1042	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	78.9582	336	1042	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.8379	324	1042	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	78.6797	319	1042	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:29:13,243] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2630/tc_result.tsv
[2023-03-17 07:29:13,243] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:29:13,243] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:29:13,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66b127ad-4c4d-4865-8af0-8c474f70b089/dqc_reference/checkm_data
[2023-03-17 07:29:13,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:29:13,248] [INFO] Task started: CheckM
[2023-03-17 07:29:13,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2630/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2630/checkm_input OceanDNA-b2630/checkm_result
[2023-03-17 07:30:03,874] [INFO] Task succeeded: CheckM
[2023-03-17 07:30:03,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:30:03,876] [INFO] ===== Completeness check finished =====
[2023-03-17 07:30:03,876] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:30:03,877] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2630/markers.fasta)
[2023-03-17 07:30:03,877] [INFO] Task started: Blastn
[2023-03-17 07:30:03,877] [INFO] Running command: blastn -query OceanDNA-b2630/markers.fasta -db /var/lib/cwl/stg66b127ad-4c4d-4865-8af0-8c474f70b089/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2630/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:30:05,410] [INFO] Task succeeded: Blastn
[2023-03-17 07:30:05,411] [INFO] Selected 17 target genomes.
[2023-03-17 07:30:05,411] [INFO] Target genome list was writen to OceanDNA-b2630/target_genomes_gtdb.txt
[2023-03-17 07:30:05,625] [INFO] Task started: fastANI
[2023-03-17 07:30:05,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgd620f71b-7d51-427d-8825-e821bf638ed3/OceanDNA-b2630.fa --refList OceanDNA-b2630/target_genomes_gtdb.txt --output OceanDNA-b2630/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:30:17,478] [INFO] Task succeeded: fastANI
[2023-03-17 07:30:17,487] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:30:17,488] [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
GCA_002313585.1	s__Microbacterium sp002313585	99.942	1003	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	97.87	0.88	0.79	16	conclusive
GCA_001898325.1	s__Microbacterium sp001898325	88.7449	786	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015565955.1	s__Microbacterium schleiferi	85.9178	792	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001652465.1	s__Microbacterium chocolatum	79.8634	395	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.91	96.78	0.87	0.81	4	-
GCF_015277855.1	s__Microbacterium sp015277855	79.7318	428	1042	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	79.5314	439	1042	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	79.5189	428	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	79.5129	398	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	79.486	412	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428485.1	s__Microbacterium sp001428485	79.4802	403	1042	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	79.4332	428	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409785.1	s__Microbacterium immunditiarum	79.4213	414	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410955.1	s__Microbacterium sp013410955	79.2792	380	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014197265.1	s__Microbacterium invictum	79.2535	387	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000422405.1	s__Microbacterium luticocti	79.2266	361	1042	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	79.1307	385	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306415.1	s__Microbacterium sp001897105	78.9743	368	1042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.03	95.75	0.95	0.85	5	-
--------------------------------------------------------------------------------
[2023-03-17 07:30:17,488] [INFO] GTDB search result was written to OceanDNA-b2630/result_gtdb.tsv
[2023-03-17 07:30:17,488] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:30:17,490] [INFO] DFAST_QC result json was written to OceanDNA-b2630/dqc_result.json
[2023-03-17 07:30:17,490] [INFO] DFAST_QC completed!
[2023-03-17 07:30:17,491] [INFO] Total running time: 0h1m46s