[2024-01-25 17:40:51,135] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:51,137] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:51,137] [INFO] DQC Reference Directory: /var/lib/cwl/stg268a8c56-b341-4b90-9c78-5a8b59a46623/dqc_reference
[2024-01-25 17:40:52,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:52,367] [INFO] Task started: Prodigal
[2024-01-25 17:40:52,368] [INFO] Running command: gunzip -c /var/lib/cwl/stg9caef9d2-9197-4666-bd31-28548bd315c7/GCF_024793945.1_ASM2479394v1_genomic.fna.gz | prodigal -d GCF_024793945.1_ASM2479394v1_genomic.fna/cds.fna -a GCF_024793945.1_ASM2479394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:10,615] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:10,616] [INFO] Task started: HMMsearch
[2024-01-25 17:41:10,616] [INFO] Running command: hmmsearch --tblout GCF_024793945.1_ASM2479394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg268a8c56-b341-4b90-9c78-5a8b59a46623/dqc_reference/reference_markers.hmm GCF_024793945.1_ASM2479394v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:10,978] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:10,979] [INFO] Found 6/6 markers.
[2024-01-25 17:41:11,031] [INFO] Query marker FASTA was written to GCF_024793945.1_ASM2479394v1_genomic.fna/markers.fasta
[2024-01-25 17:41:11,032] [INFO] Task started: Blastn
[2024-01-25 17:41:11,032] [INFO] Running command: blastn -query GCF_024793945.1_ASM2479394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268a8c56-b341-4b90-9c78-5a8b59a46623/dqc_reference/reference_markers.fasta -out GCF_024793945.1_ASM2479394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:11,600] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:11,603] [INFO] Selected 28 target genomes.
[2024-01-25 17:41:11,603] [INFO] Target genome list was writen to GCF_024793945.1_ASM2479394v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:11,642] [INFO] Task started: fastANI
[2024-01-25 17:41:11,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg9caef9d2-9197-4666-bd31-28548bd315c7/GCF_024793945.1_ASM2479394v1_genomic.fna.gz --refList GCF_024793945.1_ASM2479394v1_genomic.fna/target_genomes.txt --output GCF_024793945.1_ASM2479394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:37,792] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:37,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg268a8c56-b341-4b90-9c78-5a8b59a46623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:37,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg268a8c56-b341-4b90-9c78-5a8b59a46623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:37,798] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:41:37,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:41:37,798] [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
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	78.6971	740	1673	95	below_threshold
Emticicia aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	76.6479	185	1673	95	below_threshold
Emticicia aquatica	strain=CECT 8858, type strain	GCA_923079645.1	1681835	1681835	type	True	76.2311	167	1673	95	below_threshold
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	75.9814	64	1673	95	below_threshold
Runella slithyformis	strain=DSM 19594	GCA_000218895.1	106	106	type	True	75.5391	59	1673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:37,800] [INFO] DFAST Taxonomy check result was written to GCF_024793945.1_ASM2479394v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:37,800] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:37,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:37,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg268a8c56-b341-4b90-9c78-5a8b59a46623/dqc_reference/checkm_data
[2024-01-25 17:41:37,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:37,851] [INFO] Task started: CheckM
[2024-01-25 17:41:37,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024793945.1_ASM2479394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024793945.1_ASM2479394v1_genomic.fna/checkm_input GCF_024793945.1_ASM2479394v1_genomic.fna/checkm_result
[2024-01-25 17:42:28,908] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:28,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:28,929] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:28,929] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:28,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024793945.1_ASM2479394v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:28,931] [INFO] Task started: Blastn
[2024-01-25 17:42:28,931] [INFO] Running command: blastn -query GCF_024793945.1_ASM2479394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268a8c56-b341-4b90-9c78-5a8b59a46623/dqc_reference/reference_markers_gtdb.fasta -out GCF_024793945.1_ASM2479394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:29,705] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:29,710] [INFO] Selected 18 target genomes.
[2024-01-25 17:42:29,710] [INFO] Target genome list was writen to GCF_024793945.1_ASM2479394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:29,732] [INFO] Task started: fastANI
[2024-01-25 17:42:29,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg9caef9d2-9197-4666-bd31-28548bd315c7/GCF_024793945.1_ASM2479394v1_genomic.fna.gz --refList GCF_024793945.1_ASM2479394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024793945.1_ASM2479394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:46,558] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:46,563] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:46,564] [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_002855535.1	s__Emticicia sp002855535	96.0991	1541	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004168285.1	s__Emticicia sp004168285	78.6858	742	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013912375.1	s__Emticicia sp013912375	78.5918	662	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003418935.1	s__Emticicia sp003418935	78.3158	694	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644295.1	s__Emticicia aquatilis	76.6372	186	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905725.1	s__Leadbetterella sp002483125	76.1202	90	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	98.11	98.11	0.94	0.94	2	-
GCF_000218895.1	s__Runella slithyformis	75.5391	59	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:46,565] [INFO] GTDB search result was written to GCF_024793945.1_ASM2479394v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:46,566] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:46,569] [INFO] DFAST_QC result json was written to GCF_024793945.1_ASM2479394v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:46,570] [INFO] DFAST_QC completed!
[2024-01-25 17:42:46,570] [INFO] Total running time: 0h1m55s