[2023-06-30 10:57:46,404] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:57:46,406] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:57:46,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f913621-814e-48c1-909f-1be377217903/dqc_reference
[2023-06-30 10:57:47,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:57:47,682] [INFO] Task started: Prodigal
[2023-06-30 10:57:47,682] [INFO] Running command: gunzip -c /var/lib/cwl/stga2f7914f-1da5-4a1c-a62c-1e73930cd753/GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna.gz | prodigal -d GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/cds.fna -a GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:57:49,073] [INFO] Task succeeded: Prodigal
[2023-06-30 10:57:49,073] [INFO] Task started: HMMsearch
[2023-06-30 10:57:49,073] [INFO] Running command: hmmsearch --tblout GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f913621-814e-48c1-909f-1be377217903/dqc_reference/reference_markers.hmm GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:57:49,182] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:57:49,184] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga2f7914f-1da5-4a1c-a62c-1e73930cd753/GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna.gz]
[2023-06-30 10:57:49,196] [INFO] Query marker FASTA was written to GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/markers.fasta
[2023-06-30 10:57:49,197] [INFO] Task started: Blastn
[2023-06-30 10:57:49,197] [INFO] Running command: blastn -query GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f913621-814e-48c1-909f-1be377217903/dqc_reference/reference_markers.fasta -out GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:57:49,686] [INFO] Task succeeded: Blastn
[2023-06-30 10:57:49,690] [INFO] Selected 5 target genomes.
[2023-06-30 10:57:49,690] [INFO] Target genome list was writen to GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/target_genomes.txt
[2023-06-30 10:57:49,692] [INFO] Task started: fastANI
[2023-06-30 10:57:49,693] [INFO] Running command: fastANI --query /var/lib/cwl/stga2f7914f-1da5-4a1c-a62c-1e73930cd753/GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna.gz --refList GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/target_genomes.txt --output GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:57:51,770] [INFO] Task succeeded: fastANI
[2023-06-30 10:57:51,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f913621-814e-48c1-909f-1be377217903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:57:51,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f913621-814e-48c1-909f-1be377217903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:57:51,772] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:57:51,772] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:57:51,772] [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
--------------------------------------------------------------------------------
[2023-06-30 10:57:51,774] [INFO] DFAST Taxonomy check result was written to GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/tc_result.tsv
[2023-06-30 10:57:51,775] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:57:51,775] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:57:51,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f913621-814e-48c1-909f-1be377217903/dqc_reference/checkm_data
[2023-06-30 10:57:51,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:57:51,788] [INFO] Task started: CheckM
[2023-06-30 10:57:51,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/checkm_input GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/checkm_result
[2023-06-30 10:58:03,397] [INFO] Task succeeded: CheckM
[2023-06-30 10:58:03,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:58:03,417] [INFO] ===== Completeness check finished =====
[2023-06-30 10:58:03,417] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:58:03,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/markers.fasta)
[2023-06-30 10:58:03,418] [INFO] Task started: Blastn
[2023-06-30 10:58:03,418] [INFO] Running command: blastn -query GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f913621-814e-48c1-909f-1be377217903/dqc_reference/reference_markers_gtdb.fasta -out GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:58:04,006] [INFO] Task succeeded: Blastn
[2023-06-30 10:58:04,010] [INFO] Selected 8 target genomes.
[2023-06-30 10:58:04,011] [INFO] Target genome list was writen to GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:58:04,052] [INFO] Task started: fastANI
[2023-06-30 10:58:04,052] [INFO] Running command: fastANI --query /var/lib/cwl/stga2f7914f-1da5-4a1c-a62c-1e73930cd753/GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna.gz --refList GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/target_genomes_gtdb.txt --output GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:58:05,698] [INFO] Task succeeded: fastANI
[2023-06-30 10:58:05,705] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:58:05,705] [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
GCA_903899375.1	s__PALSA-747 sp903899375	98.1169	108	156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.46	99.00	0.86	0.79	59	conclusive
GCA_903827345.1	s__PALSA-747 sp903827345	88.7005	89	156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	97.69	97.69	0.77	0.77	2	-
GCA_903867285.1	s__PALSA-747 sp903867285	84.1552	77	156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.56	98.05	0.76	0.69	12	-
GCA_903933585.1	s__PALSA-747 sp903933585	83.4331	98	156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.42	99.37	0.91	0.88	4	-
GCA_903891755.1	s__PALSA-747 sp903891755	79.4582	50	156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.94	98.90	0.76	0.73	3	-
--------------------------------------------------------------------------------
[2023-06-30 10:58:05,708] [INFO] GTDB search result was written to GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/result_gtdb.tsv
[2023-06-30 10:58:05,708] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:58:05,712] [INFO] DFAST_QC result json was written to GCA_903995045.1_freshwater_SAG_---_SB-2103-994-D19_genomic.fna/dqc_result.json
[2023-06-30 10:58:05,712] [INFO] DFAST_QC completed!
[2023-06-30 10:58:05,712] [INFO] Total running time: 0h0m19s