[2023-03-15 06:35:36,165] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:35:36,167] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:35:36,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg51be0be5-ea54-4b07-a128-436f296b862a/dqc_reference
[2023-03-15 06:35:37,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:35:37,322] [INFO] Task started: Prodigal
[2023-03-15 06:35:37,322] [INFO] Running command: cat /var/lib/cwl/stg61de3e08-f47e-4bab-aa7b-aa13221a5cac/OceanDNA-b2586.fa | prodigal -d OceanDNA-b2586/cds.fna -a OceanDNA-b2586/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:35:54,226] [INFO] Task succeeded: Prodigal
[2023-03-15 06:35:54,227] [INFO] Task started: HMMsearch
[2023-03-15 06:35:54,227] [INFO] Running command: hmmsearch --tblout OceanDNA-b2586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51be0be5-ea54-4b07-a128-436f296b862a/dqc_reference/reference_markers.hmm OceanDNA-b2586/protein.faa > /dev/null
[2023-03-15 06:35:54,400] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:35:54,400] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg61de3e08-f47e-4bab-aa7b-aa13221a5cac/OceanDNA-b2586.fa]
[2023-03-15 06:35:54,434] [INFO] Query marker FASTA was written to OceanDNA-b2586/markers.fasta
[2023-03-15 06:35:54,435] [INFO] Task started: Blastn
[2023-03-15 06:35:54,435] [INFO] Running command: blastn -query OceanDNA-b2586/markers.fasta -db /var/lib/cwl/stg51be0be5-ea54-4b07-a128-436f296b862a/dqc_reference/reference_markers.fasta -out OceanDNA-b2586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:35:55,364] [INFO] Task succeeded: Blastn
[2023-03-15 06:35:55,368] [INFO] Selected 19 target genomes.
[2023-03-15 06:35:55,368] [INFO] Target genome list was writen to OceanDNA-b2586/target_genomes.txt
[2023-03-15 06:35:55,377] [INFO] Task started: fastANI
[2023-03-15 06:35:55,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg61de3e08-f47e-4bab-aa7b-aa13221a5cac/OceanDNA-b2586.fa --refList OceanDNA-b2586/target_genomes.txt --output OceanDNA-b2586/fastani_result.tsv --threads 1
[2023-03-15 06:36:08,978] [INFO] Task succeeded: fastANI
[2023-03-15 06:36:08,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51be0be5-ea54-4b07-a128-436f296b862a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:36:08,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51be0be5-ea54-4b07-a128-436f296b862a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:36:08,989] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:36:08,989] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:36:08,989] [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	79.9024	414	907	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	79.4638	384	907	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	79.4389	397	907	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.4213	380	907	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	79.4083	379	907	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	79.3976	378	907	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	79.3584	381	907	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.325	355	907	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	79.2859	354	907	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	79.2564	376	907	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.2551	347	907	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	79.2301	370	907	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	79.2191	375	907	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.212	349	907	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	79.1945	403	907	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.1457	375	907	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	79.1244	370	907	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.0984	392	907	95	below_threshold
Microbacterium mangrovi	strain=MUSC 115	GCA_000802305.1	1348253	1348253	type	True	78.6681	311	907	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:36:08,992] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2586/tc_result.tsv
[2023-03-15 06:36:09,000] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:36:09,000] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:36:09,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51be0be5-ea54-4b07-a128-436f296b862a/dqc_reference/checkm_data
[2023-03-15 06:36:09,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:36:09,030] [INFO] Task started: CheckM
[2023-03-15 06:36:09,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2586/checkm_input OceanDNA-b2586/checkm_result
[2023-03-15 06:36:53,389] [INFO] Task succeeded: CheckM
[2023-03-15 06:36:53,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:36:53,399] [INFO] ===== Completeness check finished =====
[2023-03-15 06:36:53,399] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:36:53,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2586/markers.fasta)
[2023-03-15 06:36:53,400] [INFO] Task started: Blastn
[2023-03-15 06:36:53,400] [INFO] Running command: blastn -query OceanDNA-b2586/markers.fasta -db /var/lib/cwl/stg51be0be5-ea54-4b07-a128-436f296b862a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:36:54,958] [INFO] Task succeeded: Blastn
[2023-03-15 06:36:54,964] [INFO] Selected 12 target genomes.
[2023-03-15 06:36:54,965] [INFO] Target genome list was writen to OceanDNA-b2586/target_genomes_gtdb.txt
[2023-03-15 06:36:55,003] [INFO] Task started: fastANI
[2023-03-15 06:36:55,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg61de3e08-f47e-4bab-aa7b-aa13221a5cac/OceanDNA-b2586.fa --refList OceanDNA-b2586/target_genomes_gtdb.txt --output OceanDNA-b2586/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:37:03,069] [INFO] Task succeeded: fastANI
[2023-03-15 06:37:03,076] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:37:03,077] [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_015565955.1	s__Microbacterium schleiferi	96.704	769	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002313585.1	s__Microbacterium sp002313585	85.4463	683	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	97.87	0.88	0.79	16	-
GCA_001898325.1	s__Microbacterium sp001898325	85.0878	681	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208045.1	s__Microbacterium thalassium	79.8886	415	907	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	79.6367	385	907	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	79.5141	376	907	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	79.4618	341	907	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	79.4202	380	907	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	79.2704	358	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999995.1	s__Microbacterium sp003999995	79.2301	370	907	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	79.1096	400	907	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	79.0871	373	907	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 06:37:03,080] [INFO] GTDB search result was written to OceanDNA-b2586/result_gtdb.tsv
[2023-03-15 06:37:03,082] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:37:03,087] [INFO] DFAST_QC result json was written to OceanDNA-b2586/dqc_result.json
[2023-03-15 06:37:03,087] [INFO] DFAST_QC completed!
[2023-03-15 06:37:03,087] [INFO] Total running time: 0h1m27s