[2023-03-17 04:15:16,797] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:16,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:16,797] [INFO] DQC Reference Directory: /var/lib/cwl/stgf09c236b-4a82-4a5f-82c5-c03c9ad6b17d/dqc_reference
[2023-03-17 04:15:18,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:18,160] [INFO] Task started: Prodigal
[2023-03-17 04:15:18,161] [INFO] Running command: cat /var/lib/cwl/stg5ebe1860-2ca4-4387-b46e-2607c10e965d/OceanDNA-b33310.fa | prodigal -d OceanDNA-b33310/cds.fna -a OceanDNA-b33310/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:45,282] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:45,282] [INFO] Task started: HMMsearch
[2023-03-17 04:15:45,282] [INFO] Running command: hmmsearch --tblout OceanDNA-b33310/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf09c236b-4a82-4a5f-82c5-c03c9ad6b17d/dqc_reference/reference_markers.hmm OceanDNA-b33310/protein.faa > /dev/null
[2023-03-17 04:15:45,543] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:45,543] [INFO] Found 6/6 markers.
[2023-03-17 04:15:45,569] [INFO] Query marker FASTA was written to OceanDNA-b33310/markers.fasta
[2023-03-17 04:15:45,569] [INFO] Task started: Blastn
[2023-03-17 04:15:45,569] [INFO] Running command: blastn -query OceanDNA-b33310/markers.fasta -db /var/lib/cwl/stgf09c236b-4a82-4a5f-82c5-c03c9ad6b17d/dqc_reference/reference_markers.fasta -out OceanDNA-b33310/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:46,393] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:46,393] [INFO] Selected 19 target genomes.
[2023-03-17 04:15:46,394] [INFO] Target genome list was writen to OceanDNA-b33310/target_genomes.txt
[2023-03-17 04:15:46,403] [INFO] Task started: fastANI
[2023-03-17 04:15:46,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ebe1860-2ca4-4387-b46e-2607c10e965d/OceanDNA-b33310.fa --refList OceanDNA-b33310/target_genomes.txt --output OceanDNA-b33310/fastani_result.tsv --threads 1
[2023-03-17 04:16:04,943] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:04,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf09c236b-4a82-4a5f-82c5-c03c9ad6b17d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:16:04,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf09c236b-4a82-4a5f-82c5-c03c9ad6b17d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:16:04,954] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:16:04,954] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:16:04,954] [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
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	85.564	904	1361	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	83.6447	872	1361	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	83.5364	849	1361	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	83.4215	890	1361	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	83.1588	874	1361	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	83.1052	893	1361	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	83.0893	907	1361	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	82.8882	849	1361	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	82.714	790	1361	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.0008	663	1361	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	79.8596	555	1361	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.8304	659	1361	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	79.6177	568	1361	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	79.3084	406	1361	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	79.1721	359	1361	95	below_threshold
Verminephrobacter aporrectodeae subsp. tuberculatae	strain=At4	GCA_000193225.2	1110392	1110389	type	True	79.1429	354	1361	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	78.8361	486	1361	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	78.7379	486	1361	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	75.7755	115	1361	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:16:04,954] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33310/tc_result.tsv
[2023-03-17 04:16:04,954] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:16:04,955] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:16:04,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf09c236b-4a82-4a5f-82c5-c03c9ad6b17d/dqc_reference/checkm_data
[2023-03-17 04:16:04,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:16:04,961] [INFO] Task started: CheckM
[2023-03-17 04:16:04,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33310/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33310/checkm_input OceanDNA-b33310/checkm_result
[2023-03-17 04:17:48,502] [INFO] Task succeeded: CheckM
[2023-03-17 04:17:48,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:17:48,506] [INFO] ===== Completeness check finished =====
[2023-03-17 04:17:48,506] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:17:48,506] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33310/markers.fasta)
[2023-03-17 04:17:48,506] [INFO] Task started: Blastn
[2023-03-17 04:17:48,506] [INFO] Running command: blastn -query OceanDNA-b33310/markers.fasta -db /var/lib/cwl/stgf09c236b-4a82-4a5f-82c5-c03c9ad6b17d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33310/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:17:50,056] [INFO] Task succeeded: Blastn
[2023-03-17 04:17:50,057] [INFO] Selected 16 target genomes.
[2023-03-17 04:17:50,057] [INFO] Target genome list was writen to OceanDNA-b33310/target_genomes_gtdb.txt
[2023-03-17 04:17:50,224] [INFO] Task started: fastANI
[2023-03-17 04:17:50,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ebe1860-2ca4-4387-b46e-2607c10e965d/OceanDNA-b33310.fa --refList OceanDNA-b33310/target_genomes_gtdb.txt --output OceanDNA-b33310/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:18:07,977] [INFO] Task succeeded: fastANI
[2023-03-17 04:18:07,986] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:18:07,986] [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_003599455.1	s__Hydrogenophaga sp003599455	87.4289	944	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	86.416	902	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503365.1	s__Hydrogenophaga sp005503365	85.6757	970	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571225.1	s__Hydrogenophaga palleronii	85.527	907	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	84.6422	940	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428625.1	s__Hydrogenophaga sp001428625	84.5785	975	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909585.1	s__Hydrogenophaga laconesensis	84.5272	977	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009859475.1	s__Hydrogenophaga sp009859475	84.5172	945	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780385.1	s__Hydrogenophaga sp018780385	84.4887	909	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010104355.1	s__Hydrogenophaga sp010104355	84.46	903	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003241965.1	s__Hydrogenophaga sp003241965	83.9826	868	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	82.9375	709	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218755.1	s__Acidovorax sp019218755	80.1502	679	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_000400995.2	s__MR-S7 sp000400995	80.0839	618	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_000382045.1	s__Variovorax paradoxus_A	79.8633	657	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.57	98.47	0.92	0.91	6	-
GCF_900106655.1	s__Variovorax sp900106655	79.6401	643	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.15	98.06	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-17 04:18:07,986] [INFO] GTDB search result was written to OceanDNA-b33310/result_gtdb.tsv
[2023-03-17 04:18:07,987] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:18:07,988] [INFO] DFAST_QC result json was written to OceanDNA-b33310/dqc_result.json
[2023-03-17 04:18:07,989] [INFO] DFAST_QC completed!
[2023-03-17 04:18:07,989] [INFO] Total running time: 0h2m51s