[2023-03-15 05:51:32,068] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,068] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f59d460-d10e-4935-a16e-2d2e68fb10e7/dqc_reference
[2023-03-15 05:51:33,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stgcc84c7e4-8c96-433e-bdae-59e242db57e8/OceanDNA-b24008.fa | prodigal -d OceanDNA-b24008/cds.fna -a OceanDNA-b24008/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:54,028] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:54,028] [INFO] Task started: HMMsearch
[2023-03-15 05:51:54,028] [INFO] Running command: hmmsearch --tblout OceanDNA-b24008/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f59d460-d10e-4935-a16e-2d2e68fb10e7/dqc_reference/reference_markers.hmm OceanDNA-b24008/protein.faa > /dev/null
[2023-03-15 05:51:54,224] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:54,225] [INFO] Found 6/6 markers.
[2023-03-15 05:51:54,249] [INFO] Query marker FASTA was written to OceanDNA-b24008/markers.fasta
[2023-03-15 05:51:54,250] [INFO] Task started: Blastn
[2023-03-15 05:51:54,250] [INFO] Running command: blastn -query OceanDNA-b24008/markers.fasta -db /var/lib/cwl/stg4f59d460-d10e-4935-a16e-2d2e68fb10e7/dqc_reference/reference_markers.fasta -out OceanDNA-b24008/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:54,853] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:54,857] [INFO] Selected 31 target genomes.
[2023-03-15 05:51:54,857] [INFO] Target genome list was writen to OceanDNA-b24008/target_genomes.txt
[2023-03-15 05:51:54,878] [INFO] Task started: fastANI
[2023-03-15 05:51:54,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc84c7e4-8c96-433e-bdae-59e242db57e8/OceanDNA-b24008.fa --refList OceanDNA-b24008/target_genomes.txt --output OceanDNA-b24008/fastani_result.tsv --threads 1
[2023-03-15 05:52:14,152] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:14,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f59d460-d10e-4935-a16e-2d2e68fb10e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:52:14,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f59d460-d10e-4935-a16e-2d2e68fb10e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:52:14,155] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:52:14,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:52:14,156] [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	80.588	138	1115	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:52:14,157] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24008/tc_result.tsv
[2023-03-15 05:52:14,157] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:52:14,158] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:52:14,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f59d460-d10e-4935-a16e-2d2e68fb10e7/dqc_reference/checkm_data
[2023-03-15 05:52:14,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:52:14,164] [INFO] Task started: CheckM
[2023-03-15 05:52:14,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24008/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24008/checkm_input OceanDNA-b24008/checkm_result
[2023-03-15 05:53:06,891] [INFO] Task succeeded: CheckM
[2023-03-15 05:53:06,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:53:06,900] [INFO] ===== Completeness check finished =====
[2023-03-15 05:53:06,900] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:53:06,900] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24008/markers.fasta)
[2023-03-15 05:53:06,900] [INFO] Task started: Blastn
[2023-03-15 05:53:06,900] [INFO] Running command: blastn -query OceanDNA-b24008/markers.fasta -db /var/lib/cwl/stg4f59d460-d10e-4935-a16e-2d2e68fb10e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24008/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:07,920] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:07,926] [INFO] Selected 32 target genomes.
[2023-03-15 05:53:07,926] [INFO] Target genome list was writen to OceanDNA-b24008/target_genomes_gtdb.txt
[2023-03-15 05:53:07,958] [INFO] Task started: fastANI
[2023-03-15 05:53:07,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc84c7e4-8c96-433e-bdae-59e242db57e8/OceanDNA-b24008.fa --refList OceanDNA-b24008/target_genomes_gtdb.txt --output OceanDNA-b24008/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:53:25,225] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:25,230] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:53:25,230] [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	80.588	138	1115	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	78.5	122	1115	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	76.9128	112	1115	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	76.7102	71	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_001657385.1	s__Marinicaulis sp001657385	76.0823	50	1115	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	75.753	74	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:53:25,232] [INFO] GTDB search result was written to OceanDNA-b24008/result_gtdb.tsv
[2023-03-15 05:53:25,234] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:53:25,237] [INFO] DFAST_QC result json was written to OceanDNA-b24008/dqc_result.json
[2023-03-15 05:53:25,237] [INFO] DFAST_QC completed!
[2023-03-15 05:53:25,238] [INFO] Total running time: 0h1m53s