[2023-03-15 11:51:17,348] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,348] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg419962dd-8db9-43a2-8590-a3d16b205874/dqc_reference
[2023-03-15 11:51:18,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,950] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,950] [INFO] Running command: cat /var/lib/cwl/stgd295f54e-1452-4bb2-83c1-49af44304bc8/OceanDNA-b2640.fa | prodigal -d OceanDNA-b2640/cds.fna -a OceanDNA-b2640/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:32,494] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:32,494] [INFO] Task started: HMMsearch
[2023-03-15 11:51:32,494] [INFO] Running command: hmmsearch --tblout OceanDNA-b2640/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg419962dd-8db9-43a2-8590-a3d16b205874/dqc_reference/reference_markers.hmm OceanDNA-b2640/protein.faa > /dev/null
[2023-03-15 11:51:32,662] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:32,662] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd295f54e-1452-4bb2-83c1-49af44304bc8/OceanDNA-b2640.fa]
[2023-03-15 11:51:32,679] [INFO] Query marker FASTA was written to OceanDNA-b2640/markers.fasta
[2023-03-15 11:51:32,679] [INFO] Task started: Blastn
[2023-03-15 11:51:32,679] [INFO] Running command: blastn -query OceanDNA-b2640/markers.fasta -db /var/lib/cwl/stg419962dd-8db9-43a2-8590-a3d16b205874/dqc_reference/reference_markers.fasta -out OceanDNA-b2640/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:33,441] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:33,442] [INFO] Selected 18 target genomes.
[2023-03-15 11:51:33,442] [INFO] Target genome list was writen to OceanDNA-b2640/target_genomes.txt
[2023-03-15 11:51:33,453] [INFO] Task started: fastANI
[2023-03-15 11:51:33,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgd295f54e-1452-4bb2-83c1-49af44304bc8/OceanDNA-b2640.fa --refList OceanDNA-b2640/target_genomes.txt --output OceanDNA-b2640/fastani_result.tsv --threads 1
[2023-03-15 11:51:45,267] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:45,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg419962dd-8db9-43a2-8590-a3d16b205874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:45,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg419962dd-8db9-43a2-8590-a3d16b205874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:45,279] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:45,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:45,279] [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	82.2077	512	728	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	78.9437	353	728	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.6354	305	728	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	78.5746	340	728	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	78.5349	303	728	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	78.4819	324	728	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	78.4632	335	728	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	78.4506	339	728	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	78.4384	312	728	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	78.3897	280	728	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	78.3169	317	728	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	78.2726	289	728	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	78.1977	299	728	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	78.1362	270	728	95	below_threshold
Microbacterium caowuchunii	strain=ST-M6	GCA_008727755.1	2614638	2614638	type	True	78.0442	251	728	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	77.99	294	728	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	77.8682	307	728	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	77.526	229	728	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:45,280] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2640/tc_result.tsv
[2023-03-15 11:51:45,280] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:45,280] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:45,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg419962dd-8db9-43a2-8590-a3d16b205874/dqc_reference/checkm_data
[2023-03-15 11:51:45,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:45,285] [INFO] Task started: CheckM
[2023-03-15 11:51:45,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2640/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2640/checkm_input OceanDNA-b2640/checkm_result
[2023-03-15 11:52:22,698] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:22,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:22,701] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:22,701] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:22,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2640/markers.fasta)
[2023-03-15 11:52:22,702] [INFO] Task started: Blastn
[2023-03-15 11:52:22,702] [INFO] Running command: blastn -query OceanDNA-b2640/markers.fasta -db /var/lib/cwl/stg419962dd-8db9-43a2-8590-a3d16b205874/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2640/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:23,916] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:23,916] [INFO] Selected 17 target genomes.
[2023-03-15 11:52:23,916] [INFO] Target genome list was writen to OceanDNA-b2640/target_genomes_gtdb.txt
[2023-03-15 11:52:23,959] [INFO] Task started: fastANI
[2023-03-15 11:52:23,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgd295f54e-1452-4bb2-83c1-49af44304bc8/OceanDNA-b2640.fa --refList OceanDNA-b2640/target_genomes_gtdb.txt --output OceanDNA-b2640/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:35,082] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:35,092] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:52:35,092] [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_002703245.1	s__Microbacterium sp002703245	99.864	662	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015277875.1	s__Microbacterium sp900098805	82.2389	510	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.54	97.00	0.83	0.71	9	-
GCF_014208045.1	s__Microbacterium thalassium	78.9565	352	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	78.6246	335	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_014779795.1	s__Microbacterium helvum	78.6111	337	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_000956465.1	s__Microbacterium trichothecenolyticum	78.5508	337	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_017831975.1	s__Microbacterium terrae	78.5485	345	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015278255.1	s__Microbacterium hibisci	78.4757	334	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_015277855.1	s__Microbacterium sp015277855	78.4675	337	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_006783905.1	s__Microbacterium kyungheense	78.4567	326	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_016907635.1	s__Microbacterium insulae	78.4475	311	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_001984105.1	s__Microbacterium sp001984105	78.4385	270	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.34	96.71	0.91	0.85	3	-
GCF_010634855.1	s__Microbacterium sp010634855	78.295	324	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCF_008727755.1	s__Microbacterium caowuchunii	78.0285	252	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.11	97.11	0.88	0.88	2	-
GCF_900155915.1	s__Microbacterium sp900155915	77.9023	299	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_003289625.1	s__Microbacterium sp003289625	77.773	253	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.69	98.69	0.93	0.93	2	-
GCF_009758255.1	s__Microbacterium sp009758255	77.5852	238	728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:35,092] [INFO] GTDB search result was written to OceanDNA-b2640/result_gtdb.tsv
[2023-03-15 11:52:35,092] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:35,094] [INFO] DFAST_QC result json was written to OceanDNA-b2640/dqc_result.json
[2023-03-15 11:52:35,094] [INFO] DFAST_QC completed!
[2023-03-15 11:52:35,094] [INFO] Total running time: 0h1m18s