[2023-06-13 05:49:32,374] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:49:32,377] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:49:32,378] [INFO] DQC Reference Directory: /var/lib/cwl/stga495b1da-b182-48bf-a879-106563f31d8e/dqc_reference
[2023-06-13 05:49:33,775] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:49:33,776] [INFO] Task started: Prodigal
[2023-06-13 05:49:33,776] [INFO] Running command: gunzip -c /var/lib/cwl/stg324ac963-a4b3-43b3-b644-8a62952918fa/GCA_947464595.1_RE-4nov15-229_genomic.fna.gz | prodigal -d GCA_947464595.1_RE-4nov15-229_genomic.fna/cds.fna -a GCA_947464595.1_RE-4nov15-229_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:49:42,505] [INFO] Task succeeded: Prodigal
[2023-06-13 05:49:42,505] [INFO] Task started: HMMsearch
[2023-06-13 05:49:42,506] [INFO] Running command: hmmsearch --tblout GCA_947464595.1_RE-4nov15-229_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga495b1da-b182-48bf-a879-106563f31d8e/dqc_reference/reference_markers.hmm GCA_947464595.1_RE-4nov15-229_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:49:42,774] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:49:42,775] [INFO] Found 6/6 markers.
[2023-06-13 05:49:42,800] [INFO] Query marker FASTA was written to GCA_947464595.1_RE-4nov15-229_genomic.fna/markers.fasta
[2023-06-13 05:49:42,800] [INFO] Task started: Blastn
[2023-06-13 05:49:42,800] [INFO] Running command: blastn -query GCA_947464595.1_RE-4nov15-229_genomic.fna/markers.fasta -db /var/lib/cwl/stga495b1da-b182-48bf-a879-106563f31d8e/dqc_reference/reference_markers.fasta -out GCA_947464595.1_RE-4nov15-229_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:49:43,409] [INFO] Task succeeded: Blastn
[2023-06-13 05:49:43,420] [INFO] Selected 14 target genomes.
[2023-06-13 05:49:43,421] [INFO] Target genome list was writen to GCA_947464595.1_RE-4nov15-229_genomic.fna/target_genomes.txt
[2023-06-13 05:49:43,423] [INFO] Task started: fastANI
[2023-06-13 05:49:43,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg324ac963-a4b3-43b3-b644-8a62952918fa/GCA_947464595.1_RE-4nov15-229_genomic.fna.gz --refList GCA_947464595.1_RE-4nov15-229_genomic.fna/target_genomes.txt --output GCA_947464595.1_RE-4nov15-229_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:49:51,435] [INFO] Task succeeded: fastANI
[2023-06-13 05:49:51,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga495b1da-b182-48bf-a879-106563f31d8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:49:51,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga495b1da-b182-48bf-a879-106563f31d8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:49:51,442] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:49:51,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 05:49:51,443] [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
Aquirufa lenticrescens	strain=9H-EGSE	GCA_019916085.1	2696560	2696560	type	True	77.0586	100	669	95	below_threshold
Aquirufa ecclesiirivi	strain=50A-KIRBA	GCA_011250515.1	2715124	2715124	type	True	77.0519	109	669	95	below_threshold
Aquirufa beregesia	strain=50C-KIRBA	GCA_011090385.1	2516556	2516556	type	True	76.7881	116	669	95	below_threshold
Aquirufa aurantiipilula	strain=15D-MOB	GCA_019923745.1	2696561	2696561	type	True	76.7164	130	669	95	below_threshold
Aquirufa antheringensis	strain=30S-ANTBAC	GCA_004307425.1	2516559	2516559	type	True	76.5812	83	669	95	below_threshold
Aquirufa nivalisilvae	strain=59G-WUEMPEL	GCA_004307455.1	2516557	2516557	type	True	76.5787	125	669	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:49:51,445] [INFO] DFAST Taxonomy check result was written to GCA_947464595.1_RE-4nov15-229_genomic.fna/tc_result.tsv
[2023-06-13 05:49:51,445] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:49:51,445] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:49:51,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga495b1da-b182-48bf-a879-106563f31d8e/dqc_reference/checkm_data
[2023-06-13 05:49:51,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:49:51,476] [INFO] Task started: CheckM
[2023-06-13 05:49:51,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947464595.1_RE-4nov15-229_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947464595.1_RE-4nov15-229_genomic.fna/checkm_input GCA_947464595.1_RE-4nov15-229_genomic.fna/checkm_result
[2023-06-13 05:50:22,330] [INFO] Task succeeded: CheckM
[2023-06-13 05:50:22,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:50:22,354] [INFO] ===== Completeness check finished =====
[2023-06-13 05:50:22,355] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:50:22,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947464595.1_RE-4nov15-229_genomic.fna/markers.fasta)
[2023-06-13 05:50:22,356] [INFO] Task started: Blastn
[2023-06-13 05:50:22,356] [INFO] Running command: blastn -query GCA_947464595.1_RE-4nov15-229_genomic.fna/markers.fasta -db /var/lib/cwl/stga495b1da-b182-48bf-a879-106563f31d8e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947464595.1_RE-4nov15-229_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:50:23,120] [INFO] Task succeeded: Blastn
[2023-06-13 05:50:23,124] [INFO] Selected 15 target genomes.
[2023-06-13 05:50:23,124] [INFO] Target genome list was writen to GCA_947464595.1_RE-4nov15-229_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:50:23,126] [INFO] Task started: fastANI
[2023-06-13 05:50:23,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg324ac963-a4b3-43b3-b644-8a62952918fa/GCA_947464595.1_RE-4nov15-229_genomic.fna.gz --refList GCA_947464595.1_RE-4nov15-229_genomic.fna/target_genomes_gtdb.txt --output GCA_947464595.1_RE-4nov15-229_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:50:30,780] [INFO] Task succeeded: fastANI
[2023-06-13 05:50:30,793] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 05:50:30,793] [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_903933935.1	s__Aquirufa sp903933935	84.8032	525	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.55	99.55	0.94	0.94	2	-
GCA_005791165.1	s__Aquirufa sp005791165	84.7668	512	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205605.1	s__Aquirufa sp013205605	83.6924	401	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907745.1	s__Aquirufa sp903907745	77.7677	195	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	98.69	97.99	0.91	0.88	6	-
GCA_903898715.1	s__Aquirufa sp903898715	77.2495	99	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.63	99.56	0.90	0.88	3	-
GCF_011250515.1	s__Allopseudarcicella ecclesiirivi	77.0519	109	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907915.1	s__Aquirufa sp903907915	77.0302	67	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984215.1	s__Aquirufa sp017984215	76.9204	104	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.80	99.80	0.94	0.94	2	-
GCA_002479785.1	s__Aquirufa sp002479785	76.6187	67	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.96	99.96	0.93	0.93	2	-
GCA_004307455.1	s__Allopseudarcicella nivalisilvae	76.5787	125	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	97.41	97.41	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-13 05:50:30,795] [INFO] GTDB search result was written to GCA_947464595.1_RE-4nov15-229_genomic.fna/result_gtdb.tsv
[2023-06-13 05:50:30,796] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:50:30,801] [INFO] DFAST_QC result json was written to GCA_947464595.1_RE-4nov15-229_genomic.fna/dqc_result.json
[2023-06-13 05:50:30,801] [INFO] DFAST_QC completed!
[2023-06-13 05:50:30,801] [INFO] Total running time: 0h0m58s