[2023-03-17 05:39:41,238] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:39:41,238] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:39:41,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg12be26d7-3c5e-4907-b332-0f9c4d6852b3/dqc_reference
[2023-03-17 05:39:42,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:39:42,369] [INFO] Task started: Prodigal
[2023-03-17 05:39:42,369] [INFO] Running command: cat /var/lib/cwl/stge097fb34-d4a3-46a8-b2ef-2950ab557dd7/OceanDNA-b45330.fa | prodigal -d OceanDNA-b45330/cds.fna -a OceanDNA-b45330/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:39:51,556] [INFO] Task succeeded: Prodigal
[2023-03-17 05:39:51,556] [INFO] Task started: HMMsearch
[2023-03-17 05:39:51,556] [INFO] Running command: hmmsearch --tblout OceanDNA-b45330/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12be26d7-3c5e-4907-b332-0f9c4d6852b3/dqc_reference/reference_markers.hmm OceanDNA-b45330/protein.faa > /dev/null
[2023-03-17 05:39:51,726] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:39:51,727] [INFO] Found 6/6 markers.
[2023-03-17 05:39:51,738] [INFO] Query marker FASTA was written to OceanDNA-b45330/markers.fasta
[2023-03-17 05:39:51,739] [INFO] Task started: Blastn
[2023-03-17 05:39:51,740] [INFO] Running command: blastn -query OceanDNA-b45330/markers.fasta -db /var/lib/cwl/stg12be26d7-3c5e-4907-b332-0f9c4d6852b3/dqc_reference/reference_markers.fasta -out OceanDNA-b45330/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:39:52,361] [INFO] Task succeeded: Blastn
[2023-03-17 05:39:52,362] [INFO] Selected 22 target genomes.
[2023-03-17 05:39:52,362] [INFO] Target genome list was writen to OceanDNA-b45330/target_genomes.txt
[2023-03-17 05:39:52,375] [INFO] Task started: fastANI
[2023-03-17 05:39:52,376] [INFO] Running command: fastANI --query /var/lib/cwl/stge097fb34-d4a3-46a8-b2ef-2950ab557dd7/OceanDNA-b45330.fa --refList OceanDNA-b45330/target_genomes.txt --output OceanDNA-b45330/fastani_result.tsv --threads 1
[2023-03-17 05:40:10,452] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:10,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12be26d7-3c5e-4907-b332-0f9c4d6852b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:40:10,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12be26d7-3c5e-4907-b332-0f9c4d6852b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:40:10,457] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:40:10,457] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:40:10,457] [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
Pontiella sulfatireligans	strain=F21(T)	GCA_900890705.1	2750658	2750658	type	True	79.128	283	485	95	below_threshold
Pontiella desulfatans	strain=F1(T)	GCA_900890425.1	2750659	2750659	type	True	79.0561	283	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:40:10,459] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45330/tc_result.tsv
[2023-03-17 05:40:10,459] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:40:10,459] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:40:10,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12be26d7-3c5e-4907-b332-0f9c4d6852b3/dqc_reference/checkm_data
[2023-03-17 05:40:10,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:40:10,465] [INFO] Task started: CheckM
[2023-03-17 05:40:10,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45330/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45330/checkm_input OceanDNA-b45330/checkm_result
[2023-03-17 05:40:37,559] [INFO] Task succeeded: CheckM
[2023-03-17 05:40:37,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:40:37,641] [INFO] ===== Completeness check finished =====
[2023-03-17 05:40:37,641] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:40:37,641] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45330/markers.fasta)
[2023-03-17 05:40:37,642] [INFO] Task started: Blastn
[2023-03-17 05:40:37,642] [INFO] Running command: blastn -query OceanDNA-b45330/markers.fasta -db /var/lib/cwl/stg12be26d7-3c5e-4907-b332-0f9c4d6852b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45330/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:40:38,721] [INFO] Task succeeded: Blastn
[2023-03-17 05:40:38,722] [INFO] Selected 16 target genomes.
[2023-03-17 05:40:38,722] [INFO] Target genome list was writen to OceanDNA-b45330/target_genomes_gtdb.txt
[2023-03-17 05:40:38,805] [INFO] Task started: fastANI
[2023-03-17 05:40:38,805] [INFO] Running command: fastANI --query /var/lib/cwl/stge097fb34-d4a3-46a8-b2ef-2950ab557dd7/OceanDNA-b45330.fa --refList OceanDNA-b45330/target_genomes_gtdb.txt --output OceanDNA-b45330/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:40:49,915] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:49,923] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:40:49,932] [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_900890705.1	s__Pontiella sulfatireligans	79.128	283	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900890425.1	s__Pontiella desulfatans	79.0634	282	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015486775.1	s__Pontiella sp015486775	78.6981	121	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042165.1	s__Pontiella sp013042165	78.5903	154	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246265.1	s__Pontiella sp003246265	78.0973	200	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937945.1	s__Pontiella sp016937945	77.7218	122	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	99.99	99.99	0.93	0.93	2	-
GCA_003230915.1	s__Pontiella sp003230915	77.6151	163	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729265.1	s__Pontiella sp012729265	77.176	87	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744085.1	s__Pontiella sp016744085	76.9438	114	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_003252225.1	s__Pontiella sp003252225	76.8513	130	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937035.1	s__Pontiella sp016937035	76.615	80	485	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:40:49,932] [INFO] GTDB search result was written to OceanDNA-b45330/result_gtdb.tsv
[2023-03-17 05:40:49,933] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:40:49,934] [INFO] DFAST_QC result json was written to OceanDNA-b45330/dqc_result.json
[2023-03-17 05:40:49,934] [INFO] DFAST_QC completed!
[2023-03-17 05:40:49,934] [INFO] Total running time: 0h1m9s