[2023-03-19 01:13:44,307] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a08298-9abe-4ccf-bcc1-f8b08d4a47d4/dqc_reference
[2023-03-19 01:13:45,414] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,414] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,414] [INFO] Running command: cat /var/lib/cwl/stg46cce726-dab0-4dc4-9efe-6b2506a32cf4/OceanDNA-b27552.fa | prodigal -d OceanDNA-b27552/cds.fna -a OceanDNA-b27552/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:54,498] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:54,499] [INFO] Task started: HMMsearch
[2023-03-19 01:13:54,499] [INFO] Running command: hmmsearch --tblout OceanDNA-b27552/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a08298-9abe-4ccf-bcc1-f8b08d4a47d4/dqc_reference/reference_markers.hmm OceanDNA-b27552/protein.faa > /dev/null
[2023-03-19 01:13:54,672] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:54,673] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg46cce726-dab0-4dc4-9efe-6b2506a32cf4/OceanDNA-b27552.fa]
[2023-03-19 01:13:54,689] [INFO] Query marker FASTA was written to OceanDNA-b27552/markers.fasta
[2023-03-19 01:13:54,691] [INFO] Task started: Blastn
[2023-03-19 01:13:54,691] [INFO] Running command: blastn -query OceanDNA-b27552/markers.fasta -db /var/lib/cwl/stg88a08298-9abe-4ccf-bcc1-f8b08d4a47d4/dqc_reference/reference_markers.fasta -out OceanDNA-b27552/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:55,294] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:55,295] [INFO] Selected 28 target genomes.
[2023-03-19 01:13:55,295] [INFO] Target genome list was writen to OceanDNA-b27552/target_genomes.txt
[2023-03-19 01:13:55,312] [INFO] Task started: fastANI
[2023-03-19 01:13:55,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg46cce726-dab0-4dc4-9efe-6b2506a32cf4/OceanDNA-b27552.fa --refList OceanDNA-b27552/target_genomes.txt --output OceanDNA-b27552/fastani_result.tsv --threads 1
[2023-03-19 01:14:11,688] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:11,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a08298-9abe-4ccf-bcc1-f8b08d4a47d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:11,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a08298-9abe-4ccf-bcc1-f8b08d4a47d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:11,693] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:11,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:14:11,694] [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
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.405	58	366	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.3242	53	366	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.2292	50	366	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.0836	52	366	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	75.9989	51	366	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.8315	63	366	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:14:11,694] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27552/tc_result.tsv
[2023-03-19 01:14:11,694] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:11,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:11,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a08298-9abe-4ccf-bcc1-f8b08d4a47d4/dqc_reference/checkm_data
[2023-03-19 01:14:11,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:11,815] [INFO] Task started: CheckM
[2023-03-19 01:14:11,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27552/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27552/checkm_input OceanDNA-b27552/checkm_result
[2023-03-19 01:14:40,340] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:40,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:40,343] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:40,343] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:40,343] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27552/markers.fasta)
[2023-03-19 01:14:40,344] [INFO] Task started: Blastn
[2023-03-19 01:14:40,344] [INFO] Running command: blastn -query OceanDNA-b27552/markers.fasta -db /var/lib/cwl/stg88a08298-9abe-4ccf-bcc1-f8b08d4a47d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27552/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:41,303] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:41,304] [INFO] Selected 29 target genomes.
[2023-03-19 01:14:41,304] [INFO] Target genome list was writen to OceanDNA-b27552/target_genomes_gtdb.txt
[2023-03-19 01:14:41,334] [INFO] Task started: fastANI
[2023-03-19 01:14:41,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg46cce726-dab0-4dc4-9efe-6b2506a32cf4/OceanDNA-b27552.fa --refList OceanDNA-b27552/target_genomes_gtdb.txt --output OceanDNA-b27552/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:57,893] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:57,902] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:57,902] [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_009762325.1	s__Roseovarius faecimaris	76.724	53	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	76.5698	63	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.5493	54	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	76.536	52	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	76.4636	55	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.4628	52	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_900109035.1	s__Cribrihabitans marinus	76.3973	56	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_001650895.1	s__EhC02 sp001650895	76.315	53	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	76.2966	52	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	76.2292	50	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	76.1569	59	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803475.1	s__Aliishimia ponticola	76.0836	52	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	76.0833	57	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	76.055	53	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_004360145.1	s__Aliiroseovarius marinus	75.9989	51	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:57,903] [INFO] GTDB search result was written to OceanDNA-b27552/result_gtdb.tsv
[2023-03-19 01:14:57,903] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:57,904] [INFO] DFAST_QC result json was written to OceanDNA-b27552/dqc_result.json
[2023-03-19 01:14:57,904] [INFO] DFAST_QC completed!
[2023-03-19 01:14:57,904] [INFO] Total running time: 0h1m14s