[2023-03-16 05:09:10,959] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:10,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:10,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg6baefed7-22dd-475d-bd30-ca11fd82388c/dqc_reference
[2023-03-16 05:09:12,060] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:12,060] [INFO] Task started: Prodigal
[2023-03-16 05:09:12,060] [INFO] Running command: cat /var/lib/cwl/stg4c832c2a-39b9-4142-8c88-88e736390fc7/OceanDNA-b27563.fa | prodigal -d OceanDNA-b27563/cds.fna -a OceanDNA-b27563/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:21,404] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:21,404] [INFO] Task started: HMMsearch
[2023-03-16 05:09:21,404] [INFO] Running command: hmmsearch --tblout OceanDNA-b27563/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6baefed7-22dd-475d-bd30-ca11fd82388c/dqc_reference/reference_markers.hmm OceanDNA-b27563/protein.faa > /dev/null
[2023-03-16 05:09:21,565] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:21,566] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4c832c2a-39b9-4142-8c88-88e736390fc7/OceanDNA-b27563.fa]
[2023-03-16 05:09:21,582] [INFO] Query marker FASTA was written to OceanDNA-b27563/markers.fasta
[2023-03-16 05:09:21,582] [INFO] Task started: Blastn
[2023-03-16 05:09:21,582] [INFO] Running command: blastn -query OceanDNA-b27563/markers.fasta -db /var/lib/cwl/stg6baefed7-22dd-475d-bd30-ca11fd82388c/dqc_reference/reference_markers.fasta -out OceanDNA-b27563/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:22,049] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:22,050] [INFO] Selected 24 target genomes.
[2023-03-16 05:09:22,050] [INFO] Target genome list was writen to OceanDNA-b27563/target_genomes.txt
[2023-03-16 05:09:22,060] [INFO] Task started: fastANI
[2023-03-16 05:09:22,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c832c2a-39b9-4142-8c88-88e736390fc7/OceanDNA-b27563.fa --refList OceanDNA-b27563/target_genomes.txt --output OceanDNA-b27563/fastani_result.tsv --threads 1
[2023-03-16 05:09:36,556] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:36,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6baefed7-22dd-475d-bd30-ca11fd82388c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:36,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6baefed7-22dd-475d-bd30-ca11fd82388c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:36,563] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:09:36,563] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:09:36,563] [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
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.6156	63	392	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.3547	59	392	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3486	61	392	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3425	60	392	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.2311	50	392	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.2298	52	392	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	76.1409	60	392	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	75.9627	54	392	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:09:36,563] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27563/tc_result.tsv
[2023-03-16 05:09:36,563] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:36,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:36,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6baefed7-22dd-475d-bd30-ca11fd82388c/dqc_reference/checkm_data
[2023-03-16 05:09:36,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:36,568] [INFO] Task started: CheckM
[2023-03-16 05:09:36,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27563/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27563/checkm_input OceanDNA-b27563/checkm_result
[2023-03-16 05:10:04,609] [INFO] Task succeeded: CheckM
[2023-03-16 05:10:04,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:10:04,612] [INFO] ===== Completeness check finished =====
[2023-03-16 05:10:04,613] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:10:04,613] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27563/markers.fasta)
[2023-03-16 05:10:04,614] [INFO] Task started: Blastn
[2023-03-16 05:10:04,614] [INFO] Running command: blastn -query OceanDNA-b27563/markers.fasta -db /var/lib/cwl/stg6baefed7-22dd-475d-bd30-ca11fd82388c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27563/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:10:05,121] [INFO] Task succeeded: Blastn
[2023-03-16 05:10:05,122] [INFO] Selected 25 target genomes.
[2023-03-16 05:10:05,122] [INFO] Target genome list was writen to OceanDNA-b27563/target_genomes_gtdb.txt
[2023-03-16 05:10:05,149] [INFO] Task started: fastANI
[2023-03-16 05:10:05,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c832c2a-39b9-4142-8c88-88e736390fc7/OceanDNA-b27563.fa --refList OceanDNA-b27563/target_genomes_gtdb.txt --output OceanDNA-b27563/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:10:19,511] [INFO] Task succeeded: fastANI
[2023-03-16 05:10:19,518] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:10:19,518] [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_000161775.1	s__Ruegeria lacuscaerulensis	76.8833	60	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013032855.1	s__Ruegeria arenilitoris	76.6269	61	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_900129345.1	s__Ruegeria intermedia	76.6156	63	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	76.5432	58	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	76.5368	70	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799325.1	s__Thalassobius vesicularis	76.4131	57	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.3425	60	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	76.294	54	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_005938215.1	s__Ruegeria sediminis	76.2311	50	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401465.1	s__Aestuariivita sp018401465	76.177	50	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.0128	65	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	76.007	56	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:10:19,519] [INFO] GTDB search result was written to OceanDNA-b27563/result_gtdb.tsv
[2023-03-16 05:10:19,519] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:10:19,521] [INFO] DFAST_QC result json was written to OceanDNA-b27563/dqc_result.json
[2023-03-16 05:10:19,521] [INFO] DFAST_QC completed!
[2023-03-16 05:10:19,521] [INFO] Total running time: 0h1m9s