[2024-01-24 14:14:00,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgc080cbb8-da30-43eb-91da-ff76bca19a80/dqc_reference
[2024-01-24 14:14:01,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:01,784] [INFO] Task started: Prodigal
[2024-01-24 14:14:01,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg9257d005-ba5e-4c29-95e2-7630ffcb98bd/GCF_030056595.1_ASM3005659v1_genomic.fna.gz | prodigal -d GCF_030056595.1_ASM3005659v1_genomic.fna/cds.fna -a GCF_030056595.1_ASM3005659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:32,993] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:32,993] [INFO] Task started: HMMsearch
[2024-01-24 14:14:32,993] [INFO] Running command: hmmsearch --tblout GCF_030056595.1_ASM3005659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc080cbb8-da30-43eb-91da-ff76bca19a80/dqc_reference/reference_markers.hmm GCF_030056595.1_ASM3005659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,477] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,576] [INFO] Query marker FASTA was written to GCF_030056595.1_ASM3005659v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,577] [INFO] Task started: Blastn
[2024-01-24 14:14:33,577] [INFO] Running command: blastn -query GCF_030056595.1_ASM3005659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc080cbb8-da30-43eb-91da-ff76bca19a80/dqc_reference/reference_markers.fasta -out GCF_030056595.1_ASM3005659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:34,709] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:34,718] [INFO] Selected 20 target genomes.
[2024-01-24 14:14:34,718] [INFO] Target genome list was writen to GCF_030056595.1_ASM3005659v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:34,732] [INFO] Task started: fastANI
[2024-01-24 14:14:34,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg9257d005-ba5e-4c29-95e2-7630ffcb98bd/GCF_030056595.1_ASM3005659v1_genomic.fna.gz --refList GCF_030056595.1_ASM3005659v1_genomic.fna/target_genomes.txt --output GCF_030056595.1_ASM3005659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:49,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:49,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc080cbb8-da30-43eb-91da-ff76bca19a80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:49,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc080cbb8-da30-43eb-91da-ff76bca19a80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:49,293] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:14:49,293] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:14:49,294] [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
Flectobacillus major	strain=DSM 103	GCA_000427405.1	103	103	type	True	79.2728	734	2191	95	below_threshold
Arcicella aurantiaca	strain=DSM 22214	GCA_003148625.1	591202	591202	type	True	77.1204	303	2191	95	below_threshold
Aquirufa antheringensis	strain=30S-ANTBAC	GCA_004307425.1	2516559	2516559	type	True	76.6423	52	2191	95	below_threshold
Aquirufa lenticrescens	strain=9H-EGSE	GCA_019916085.1	2696560	2696560	type	True	76.3685	67	2191	95	below_threshold
Aquirufa aurantiipilula	strain=15D-MOB	GCA_019923745.1	2696561	2696561	type	True	76.0405	68	2191	95	below_threshold
Sandaracinomonas limnophila	strain=FSY-15	GCA_004005965.1	1862386	1862386	type	True	76.0152	80	2191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:49,296] [INFO] DFAST Taxonomy check result was written to GCF_030056595.1_ASM3005659v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:49,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:49,297] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:49,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc080cbb8-da30-43eb-91da-ff76bca19a80/dqc_reference/checkm_data
[2024-01-24 14:14:49,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:49,370] [INFO] Task started: CheckM
[2024-01-24 14:14:49,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030056595.1_ASM3005659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030056595.1_ASM3005659v1_genomic.fna/checkm_input GCF_030056595.1_ASM3005659v1_genomic.fna/checkm_result
[2024-01-24 14:16:07,622] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:07,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:07,647] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:07,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:07,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030056595.1_ASM3005659v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:07,650] [INFO] Task started: Blastn
[2024-01-24 14:16:07,651] [INFO] Running command: blastn -query GCF_030056595.1_ASM3005659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc080cbb8-da30-43eb-91da-ff76bca19a80/dqc_reference/reference_markers_gtdb.fasta -out GCF_030056595.1_ASM3005659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:08,442] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:08,447] [INFO] Selected 15 target genomes.
[2024-01-24 14:16:08,447] [INFO] Target genome list was writen to GCF_030056595.1_ASM3005659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:08,458] [INFO] Task started: fastANI
[2024-01-24 14:16:08,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg9257d005-ba5e-4c29-95e2-7630ffcb98bd/GCF_030056595.1_ASM3005659v1_genomic.fna.gz --refList GCF_030056595.1_ASM3005659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030056595.1_ASM3005659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:26,099] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:26,108] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:26,109] [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_002270355.1	s__Flectobacillus sp002270355	96.689	1949	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	97.63	97.63	0.89	0.89	2	conclusive
GCF_009905545.1	s__Flectobacillus sp009905545	90.7761	1896	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427405.1	s__Flectobacillus major	79.2972	731	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298025.1	s__Flectobacillus sp013298025	78.3622	442	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204325.1	s__Arcicella rosea	77.1626	338	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148625.1	s__Arcicella aurantiaca	77.1292	302	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115665.1	s__Pseudarcicella hirudinis	76.4884	158	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Pseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298125.1	s__Arcicella sp013298125	76.2647	184	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298865.1	s__JAAFJL01 sp013298865	76.0623	160	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__JAAFJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376355.1	s__Arcicella sp014376355	75.962	134	2191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:26,110] [INFO] GTDB search result was written to GCF_030056595.1_ASM3005659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:26,111] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:26,116] [INFO] DFAST_QC result json was written to GCF_030056595.1_ASM3005659v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:26,116] [INFO] DFAST_QC completed!
[2024-01-24 14:16:26,116] [INFO] Total running time: 0h2m26s