[2023-03-15 15:55:16,218] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,218] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,218] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d326fb8-ec93-4a2a-a841-4bd22f58a8bf/dqc_reference
[2023-03-15 15:55:17,917] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,917] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,917] [INFO] Running command: cat /var/lib/cwl/stgbf26d328-a846-4a1c-b98a-e330ed702552/OceanDNA-b2784.fa | prodigal -d OceanDNA-b2784/cds.fna -a OceanDNA-b2784/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:25,446] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:25,446] [INFO] Task started: HMMsearch
[2023-03-15 15:55:25,446] [INFO] Running command: hmmsearch --tblout OceanDNA-b2784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d326fb8-ec93-4a2a-a841-4bd22f58a8bf/dqc_reference/reference_markers.hmm OceanDNA-b2784/protein.faa > /dev/null
[2023-03-15 15:55:25,611] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:25,612] [INFO] Found 6/6 markers.
[2023-03-15 15:55:25,628] [INFO] Query marker FASTA was written to OceanDNA-b2784/markers.fasta
[2023-03-15 15:55:25,629] [INFO] Task started: Blastn
[2023-03-15 15:55:25,629] [INFO] Running command: blastn -query OceanDNA-b2784/markers.fasta -db /var/lib/cwl/stg8d326fb8-ec93-4a2a-a841-4bd22f58a8bf/dqc_reference/reference_markers.fasta -out OceanDNA-b2784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:26,677] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:26,678] [INFO] Selected 25 target genomes.
[2023-03-15 15:55:26,678] [INFO] Target genome list was writen to OceanDNA-b2784/target_genomes.txt
[2023-03-15 15:55:26,698] [INFO] Task started: fastANI
[2023-03-15 15:55:26,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf26d328-a846-4a1c-b98a-e330ed702552/OceanDNA-b2784.fa --refList OceanDNA-b2784/target_genomes.txt --output OceanDNA-b2784/fastani_result.tsv --threads 1
[2023-03-15 15:55:38,860] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:38,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d326fb8-ec93-4a2a-a841-4bd22f58a8bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:38,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d326fb8-ec93-4a2a-a841-4bd22f58a8bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:38,875] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:38,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:55:38,875] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.909	207	334	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.615	174	334	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	78.8055	143	334	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	78.7708	144	334	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.2387	129	334	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.2092	130	334	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	78.1652	150	334	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.156	162	334	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	78.0817	164	334	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	77.9577	140	334	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	77.9388	105	334	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	77.7924	141	334	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	77.739	127	334	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	77.7348	135	334	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.7335	147	334	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	77.6918	132	334	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	77.595	129	334	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	77.5362	131	334	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	77.4525	118	334	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	77.4266	145	334	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	77.4035	120	334	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	77.3783	140	334	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	77.3182	144	334	95	below_threshold
Marisediminicola antarctica	strain=ZS314	GCA_009930795.1	674079	674079	type	True	77.2561	122	334	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	77.0	114	334	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:38,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2784/tc_result.tsv
[2023-03-15 15:55:38,876] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:38,876] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:38,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d326fb8-ec93-4a2a-a841-4bd22f58a8bf/dqc_reference/checkm_data
[2023-03-15 15:55:38,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:38,880] [INFO] Task started: CheckM
[2023-03-15 15:55:38,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2784/checkm_input OceanDNA-b2784/checkm_result
[2023-03-15 15:56:02,876] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:02,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.03%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:02,878] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:02,879] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:02,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2784/markers.fasta)
[2023-03-15 15:56:02,879] [INFO] Task started: Blastn
[2023-03-15 15:56:02,879] [INFO] Running command: blastn -query OceanDNA-b2784/markers.fasta -db /var/lib/cwl/stg8d326fb8-ec93-4a2a-a841-4bd22f58a8bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:04,550] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:04,551] [INFO] Selected 16 target genomes.
[2023-03-15 15:56:04,551] [INFO] Target genome list was writen to OceanDNA-b2784/target_genomes_gtdb.txt
[2023-03-15 15:56:04,559] [INFO] Task started: fastANI
[2023-03-15 15:56:04,560] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf26d328-a846-4a1c-b98a-e330ed702552/OceanDNA-b2784.fa --refList OceanDNA-b2784/target_genomes_gtdb.txt --output OceanDNA-b2784/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:12,571] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:12,581] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:12,581] [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_014653215.1	s__Pseudolysinimonas yzui	84.5635	255	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	80.2174	186	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	80.0164	201	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	79.9871	204	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308515.1	s__Pseudolysinimonas sp017308515	79.8275	200	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	79.7611	188	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008365275.1	s__Protaetiibacter larvae	79.615	174	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216815.1	s__Protaetiibacter sp004216815	79.6148	174	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479755.1	s__Pseudolysinimonas sp905479755	79.3409	156	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	79.3277	159	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	78.9507	161	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	78.7374	172	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371975.2	s__Marinisubtilis pacificus	78.4119	143	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	-
GCA_005502445.1	s__Yonghaparkia sp005502445	78.3307	143	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355695.1	s__Clavibacter nebraskensis	77.8824	126	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.97	99.95	1.00	1.00	6	-
GCF_015351075.1	s__Clavibacter sp015351075	77.7247	137	334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:12,582] [INFO] GTDB search result was written to OceanDNA-b2784/result_gtdb.tsv
[2023-03-15 15:56:12,582] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:12,584] [INFO] DFAST_QC result json was written to OceanDNA-b2784/dqc_result.json
[2023-03-15 15:56:12,584] [INFO] DFAST_QC completed!
[2023-03-15 15:56:12,584] [INFO] Total running time: 0h0m56s