[2024-01-24 11:44:38,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb19944e-926a-432f-9384-7a3cfa2230af/dqc_reference
[2024-01-24 11:44:41,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,486] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a84bb06-7399-45fe-83b8-0ddb172c62ed/GCF_003148625.1_ASM314862v1_genomic.fna.gz | prodigal -d GCF_003148625.1_ASM314862v1_genomic.fna/cds.fna -a GCF_003148625.1_ASM314862v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:45:04,727] [INFO] Task succeeded: Prodigal
[2024-01-24 11:45:04,728] [INFO] Task started: HMMsearch
[2024-01-24 11:45:04,728] [INFO] Running command: hmmsearch --tblout GCF_003148625.1_ASM314862v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb19944e-926a-432f-9384-7a3cfa2230af/dqc_reference/reference_markers.hmm GCF_003148625.1_ASM314862v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:45:05,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:45:05,032] [INFO] Found 6/6 markers.
[2024-01-24 11:45:05,080] [INFO] Query marker FASTA was written to GCF_003148625.1_ASM314862v1_genomic.fna/markers.fasta
[2024-01-24 11:45:05,080] [INFO] Task started: Blastn
[2024-01-24 11:45:05,081] [INFO] Running command: blastn -query GCF_003148625.1_ASM314862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb19944e-926a-432f-9384-7a3cfa2230af/dqc_reference/reference_markers.fasta -out GCF_003148625.1_ASM314862v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:05,665] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:05,670] [INFO] Selected 18 target genomes.
[2024-01-24 11:45:05,670] [INFO] Target genome list was writen to GCF_003148625.1_ASM314862v1_genomic.fna/target_genomes.txt
[2024-01-24 11:45:05,678] [INFO] Task started: fastANI
[2024-01-24 11:45:05,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a84bb06-7399-45fe-83b8-0ddb172c62ed/GCF_003148625.1_ASM314862v1_genomic.fna.gz --refList GCF_003148625.1_ASM314862v1_genomic.fna/target_genomes.txt --output GCF_003148625.1_ASM314862v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:18,876] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:18,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb19944e-926a-432f-9384-7a3cfa2230af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:18,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb19944e-926a-432f-9384-7a3cfa2230af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:18,893] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:18,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:18,894] [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
Arcicella aurantiaca	strain=DSM 22214	GCA_003148625.1	591202	591202	type	True	100.0	1930	1937	95	conclusive
Flectobacillus major	strain=DSM 103	GCA_000427405.1	103	103	type	True	76.919	300	1937	95	below_threshold
Aquirufa antheringensis	strain=30S-ANTBAC	GCA_004307425.1	2516559	2516559	type	True	76.412	55	1937	95	below_threshold
Emticicia aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	76.4002	221	1937	95	below_threshold
Aquirufa rosea	strain=CAR-16	GCA_004118285.1	2509241	2509241	type	True	76.351	61	1937	95	below_threshold
Sandaracinomonas limnophila	strain=FSY-15	GCA_004005965.1	1862386	1862386	type	True	76.2767	95	1937	95	below_threshold
Aquirufa nivalisilvae	strain=59G-WUEMPEL	GCA_004307455.1	2516557	2516557	type	True	76.2179	62	1937	95	below_threshold
Aquirufa ecclesiirivi	strain=50A-KIRBA	GCA_011250515.1	2715124	2715124	type	True	75.9532	75	1937	95	below_threshold
Aquirufa aurantiipilula	strain=15D-MOB	GCA_019923745.1	2696561	2696561	type	True	75.7905	82	1937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:18,896] [INFO] DFAST Taxonomy check result was written to GCF_003148625.1_ASM314862v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:18,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:18,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:18,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb19944e-926a-432f-9384-7a3cfa2230af/dqc_reference/checkm_data
[2024-01-24 11:45:18,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:18,959] [INFO] Task started: CheckM
[2024-01-24 11:45:18,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148625.1_ASM314862v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148625.1_ASM314862v1_genomic.fna/checkm_input GCF_003148625.1_ASM314862v1_genomic.fna/checkm_result
[2024-01-24 11:46:25,952] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:25,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:25,974] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:25,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:25,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148625.1_ASM314862v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:25,975] [INFO] Task started: Blastn
[2024-01-24 11:46:25,975] [INFO] Running command: blastn -query GCF_003148625.1_ASM314862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb19944e-926a-432f-9384-7a3cfa2230af/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148625.1_ASM314862v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:26,710] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:26,714] [INFO] Selected 11 target genomes.
[2024-01-24 11:46:26,714] [INFO] Target genome list was writen to GCF_003148625.1_ASM314862v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:26,724] [INFO] Task started: fastANI
[2024-01-24 11:46:26,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a84bb06-7399-45fe-83b8-0ddb172c62ed/GCF_003148625.1_ASM314862v1_genomic.fna.gz --refList GCF_003148625.1_ASM314862v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148625.1_ASM314862v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:38,558] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:38,575] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:38,575] [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_003148625.1	s__Arcicella aurantiaca	100.0	1930	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013298805.1	s__Arcicella sp013298805	85.1528	979	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298125.1	s__Arcicella sp013298125	79.2033	762	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376355.1	s__Arcicella sp014376355	78.7826	624	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204325.1	s__Arcicella rosea	78.4586	555	1937	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	77.3158	398	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__JAAFJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905545.1	s__Flectobacillus sp009905545	77.0197	329	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002270355.1	s__Flectobacillus sp002270355	76.8331	333	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	97.63	97.63	0.89	0.89	2	-
GCF_900115665.1	s__Pseudarcicella hirudinis	76.4833	163	1937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Pseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:38,577] [INFO] GTDB search result was written to GCF_003148625.1_ASM314862v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:38,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:38,582] [INFO] DFAST_QC result json was written to GCF_003148625.1_ASM314862v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:38,582] [INFO] DFAST_QC completed!
[2024-01-24 11:46:38,582] [INFO] Total running time: 0h2m0s