[2023-03-16 08:59:43,914] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:59:43,914] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:59:43,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg610c2f2c-111c-4f1d-b11a-d4efea57cf8d/dqc_reference
[2023-03-16 08:59:45,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:59:45,387] [INFO] Task started: Prodigal
[2023-03-16 08:59:45,387] [INFO] Running command: cat /var/lib/cwl/stg365c72c1-14f9-44d1-a1d8-904c3bf22d6e/OceanDNA-b33303.fa | prodigal -d OceanDNA-b33303/cds.fna -a OceanDNA-b33303/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:00:23,768] [INFO] Task succeeded: Prodigal
[2023-03-16 09:00:23,769] [INFO] Task started: HMMsearch
[2023-03-16 09:00:23,769] [INFO] Running command: hmmsearch --tblout OceanDNA-b33303/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg610c2f2c-111c-4f1d-b11a-d4efea57cf8d/dqc_reference/reference_markers.hmm OceanDNA-b33303/protein.faa > /dev/null
[2023-03-16 09:00:24,042] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:00:24,043] [INFO] Found 6/6 markers.
[2023-03-16 09:00:24,088] [INFO] Query marker FASTA was written to OceanDNA-b33303/markers.fasta
[2023-03-16 09:00:24,089] [INFO] Task started: Blastn
[2023-03-16 09:00:24,089] [INFO] Running command: blastn -query OceanDNA-b33303/markers.fasta -db /var/lib/cwl/stg610c2f2c-111c-4f1d-b11a-d4efea57cf8d/dqc_reference/reference_markers.fasta -out OceanDNA-b33303/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:00:25,012] [INFO] Task succeeded: Blastn
[2023-03-16 09:00:25,015] [INFO] Selected 13 target genomes.
[2023-03-16 09:00:25,015] [INFO] Target genome list was writen to OceanDNA-b33303/target_genomes.txt
[2023-03-16 09:00:25,022] [INFO] Task started: fastANI
[2023-03-16 09:00:25,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg365c72c1-14f9-44d1-a1d8-904c3bf22d6e/OceanDNA-b33303.fa --refList OceanDNA-b33303/target_genomes.txt --output OceanDNA-b33303/fastani_result.tsv --threads 1
[2023-03-16 09:00:40,585] [INFO] Task succeeded: fastANI
[2023-03-16 09:00:40,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg610c2f2c-111c-4f1d-b11a-d4efea57cf8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:00:40,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg610c2f2c-111c-4f1d-b11a-d4efea57cf8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:00:40,594] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 09:00:40,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 09:00:40,594] [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
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	97.7047	1698	1938	95	conclusive
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	93.0135	1520	1938	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	88.0325	1383	1938	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	87.8905	1401	1938	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	87.8689	1414	1938	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	87.8657	1404	1938	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	87.7958	1404	1938	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	87.6509	1353	1938	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	81.5734	753	1938	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	79.2951	559	1938	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	79.0939	511	1938	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	78.9739	504	1938	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	77.6113	315	1938	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:00:40,604] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33303/tc_result.tsv
[2023-03-16 09:00:40,604] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:00:40,604] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:00:40,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg610c2f2c-111c-4f1d-b11a-d4efea57cf8d/dqc_reference/checkm_data
[2023-03-16 09:00:40,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:00:40,827] [INFO] Task started: CheckM
[2023-03-16 09:00:40,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33303/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33303/checkm_input OceanDNA-b33303/checkm_result
[2023-03-16 09:02:27,928] [INFO] Task succeeded: CheckM
[2023-03-16 09:02:27,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:02:27,941] [INFO] ===== Completeness check finished =====
[2023-03-16 09:02:27,941] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:02:27,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33303/markers.fasta)
[2023-03-16 09:02:27,944] [INFO] Task started: Blastn
[2023-03-16 09:02:27,944] [INFO] Running command: blastn -query OceanDNA-b33303/markers.fasta -db /var/lib/cwl/stg610c2f2c-111c-4f1d-b11a-d4efea57cf8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33303/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:02:29,994] [INFO] Task succeeded: Blastn
[2023-03-16 09:02:30,000] [INFO] Selected 13 target genomes.
[2023-03-16 09:02:30,000] [INFO] Target genome list was writen to OceanDNA-b33303/target_genomes_gtdb.txt
[2023-03-16 09:02:30,143] [INFO] Task started: fastANI
[2023-03-16 09:02:30,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg365c72c1-14f9-44d1-a1d8-904c3bf22d6e/OceanDNA-b33303.fa --refList OceanDNA-b33303/target_genomes_gtdb.txt --output OceanDNA-b33303/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:02:44,948] [INFO] Task succeeded: fastANI
[2023-03-16 09:02:44,956] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:02:44,956] [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_004367745.1	s__Herbaspirillum huttiense	97.4412	1671	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.45	97.06	0.87	0.86	14	conclusive
GCF_002213425.1	s__Herbaspirillum aquaticum	93.0241	1519	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.01	95.53	0.89	0.85	3	-
GCF_000261365.1	s__Herbaspirillum sp000261365	90.5383	1460	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.65	98.65	0.93	0.93	2	-
GCF_001040945.1	s__Herbaspirillum seropedicae	87.8902	1411	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_003719195.1	s__Herbaspirillum rubrisubalbicans	87.8617	1405	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.49	96.58	0.87	0.83	8	-
GCF_000300975.2	s__Herbaspirillum frisingense	87.6585	1352	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.59	97.42	0.92	0.89	5	-
GCF_015767275.1	s__Herbaspirillum sp013426985	87.4863	1383	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016429215.1	s__Herbaspirillum sp016429215	87.0971	1310	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770725.1	s__Aquabacterium sp001770725	77.7237	326	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000265.1	s__Aquabacterium sp016000265	77.6146	276	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.96	99.96	0.95	0.95	2	-
GCF_004362855.1	s__Aquabacterium commune	77.5835	317	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	95.44	95.44	0.90	0.90	2	-
GCA_005502875.1	s__Aquabacterium sp005502875	77.521	304	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447195.1	s__Aquabacterium parvum	77.4358	315	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.32	96.21	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-16 09:02:44,964] [INFO] GTDB search result was written to OceanDNA-b33303/result_gtdb.tsv
[2023-03-16 09:02:44,965] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:02:44,966] [INFO] DFAST_QC result json was written to OceanDNA-b33303/dqc_result.json
[2023-03-16 09:02:44,966] [INFO] DFAST_QC completed!
[2023-03-16 09:02:44,966] [INFO] Total running time: 0h3m1s