[2023-03-16 02:38:04,952] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,952] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg23216a9d-163b-47ae-979c-989e43b58da9/dqc_reference
[2023-03-16 02:38:06,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,171] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,171] [INFO] Running command: cat /var/lib/cwl/stg5c5082e9-6339-422e-8af3-c8bacf5e90bf/OceanDNA-b24005.fa | prodigal -d OceanDNA-b24005/cds.fna -a OceanDNA-b24005/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:17,220] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:17,221] [INFO] Task started: HMMsearch
[2023-03-16 02:38:17,221] [INFO] Running command: hmmsearch --tblout OceanDNA-b24005/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23216a9d-163b-47ae-979c-989e43b58da9/dqc_reference/reference_markers.hmm OceanDNA-b24005/protein.faa > /dev/null
[2023-03-16 02:38:17,429] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:17,429] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5c5082e9-6339-422e-8af3-c8bacf5e90bf/OceanDNA-b24005.fa]
[2023-03-16 02:38:17,448] [INFO] Query marker FASTA was written to OceanDNA-b24005/markers.fasta
[2023-03-16 02:38:17,448] [INFO] Task started: Blastn
[2023-03-16 02:38:17,449] [INFO] Running command: blastn -query OceanDNA-b24005/markers.fasta -db /var/lib/cwl/stg23216a9d-163b-47ae-979c-989e43b58da9/dqc_reference/reference_markers.fasta -out OceanDNA-b24005/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:18,159] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:18,159] [INFO] Selected 23 target genomes.
[2023-03-16 02:38:18,160] [INFO] Target genome list was writen to OceanDNA-b24005/target_genomes.txt
[2023-03-16 02:38:18,172] [INFO] Task started: fastANI
[2023-03-16 02:38:18,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c5082e9-6339-422e-8af3-c8bacf5e90bf/OceanDNA-b24005.fa --refList OceanDNA-b24005/target_genomes.txt --output OceanDNA-b24005/fastani_result.tsv --threads 1
[2023-03-16 02:38:33,088] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:33,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23216a9d-163b-47ae-979c-989e43b58da9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:33,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23216a9d-163b-47ae-979c-989e43b58da9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:33,094] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:33,094] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 02:38:33,094] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	78.6462	208	572	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.7225	65	572	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.6544	69	572	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	76.6544	69	572	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	76.48	116	572	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	76.4625	117	572	95	below_threshold
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	76.3241	67	572	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	76.3241	67	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:33,095] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24005/tc_result.tsv
[2023-03-16 02:38:33,095] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:33,095] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:33,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23216a9d-163b-47ae-979c-989e43b58da9/dqc_reference/checkm_data
[2023-03-16 02:38:33,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:33,102] [INFO] Task started: CheckM
[2023-03-16 02:38:33,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24005/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24005/checkm_input OceanDNA-b24005/checkm_result
[2023-03-16 02:39:04,762] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:04,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:04,765] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:04,765] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:04,766] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24005/markers.fasta)
[2023-03-16 02:39:04,766] [INFO] Task started: Blastn
[2023-03-16 02:39:04,766] [INFO] Running command: blastn -query OceanDNA-b24005/markers.fasta -db /var/lib/cwl/stg23216a9d-163b-47ae-979c-989e43b58da9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24005/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:06,053] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:06,054] [INFO] Selected 17 target genomes.
[2023-03-16 02:39:06,054] [INFO] Target genome list was writen to OceanDNA-b24005/target_genomes_gtdb.txt
[2023-03-16 02:39:06,508] [INFO] Task started: fastANI
[2023-03-16 02:39:06,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c5082e9-6339-422e-8af3-c8bacf5e90bf/OceanDNA-b24005.fa --refList OceanDNA-b24005/target_genomes_gtdb.txt --output OceanDNA-b24005/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:17,352] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:17,360] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 02:39:17,360] [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_002943565.1	s__Marinicaulis flavus	78.6058	210	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	78.523	173	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	77.2108	167	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002388885.1	s__Marinicaulis sp002388885	77.188	158	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151255.1	s__Marinicaulis sp013151255	76.8339	118	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002535.1	s__Marinicaulis sp013002535	76.7158	100	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCF_014640095.1	s__Aquisalinus flavus	76.6544	69	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016125425.1	s__Amphiplicatus sp016125425	76.5161	107	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	76.418	99	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	76.39	102	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712425.2	s__Aquisalinus luteolus	76.3241	67	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003506635.1	s__CV81 sp003506635	76.2931	67	572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:17,360] [INFO] GTDB search result was written to OceanDNA-b24005/result_gtdb.tsv
[2023-03-16 02:39:17,360] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:17,362] [INFO] DFAST_QC result json was written to OceanDNA-b24005/dqc_result.json
[2023-03-16 02:39:17,362] [INFO] DFAST_QC completed!
[2023-03-16 02:39:17,362] [INFO] Total running time: 0h1m12s