[2024-01-25 20:12:05,701] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,703] [INFO] DQC Reference Directory: /var/lib/cwl/stge79014c8-8adf-4d98-8ba9-400671c48592/dqc_reference
[2024-01-25 20:12:06,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,921] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,921] [INFO] Running command: gunzip -c /var/lib/cwl/stgc928fa9a-5c9c-4496-9873-4e5b1edf7abc/GCF_003258705.1_ASM325870v1_genomic.fna.gz | prodigal -d GCF_003258705.1_ASM325870v1_genomic.fna/cds.fna -a GCF_003258705.1_ASM325870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:22,901] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:22,902] [INFO] Task started: HMMsearch
[2024-01-25 20:12:22,902] [INFO] Running command: hmmsearch --tblout GCF_003258705.1_ASM325870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge79014c8-8adf-4d98-8ba9-400671c48592/dqc_reference/reference_markers.hmm GCF_003258705.1_ASM325870v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:23,213] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:23,214] [INFO] Found 6/6 markers.
[2024-01-25 20:12:23,259] [INFO] Query marker FASTA was written to GCF_003258705.1_ASM325870v1_genomic.fna/markers.fasta
[2024-01-25 20:12:23,259] [INFO] Task started: Blastn
[2024-01-25 20:12:23,259] [INFO] Running command: blastn -query GCF_003258705.1_ASM325870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge79014c8-8adf-4d98-8ba9-400671c48592/dqc_reference/reference_markers.fasta -out GCF_003258705.1_ASM325870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:23,812] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:23,815] [INFO] Selected 28 target genomes.
[2024-01-25 20:12:23,815] [INFO] Target genome list was writen to GCF_003258705.1_ASM325870v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:23,861] [INFO] Task started: fastANI
[2024-01-25 20:12:23,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgc928fa9a-5c9c-4496-9873-4e5b1edf7abc/GCF_003258705.1_ASM325870v1_genomic.fna.gz --refList GCF_003258705.1_ASM325870v1_genomic.fna/target_genomes.txt --output GCF_003258705.1_ASM325870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:47,252] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:47,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge79014c8-8adf-4d98-8ba9-400671c48592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:47,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge79014c8-8adf-4d98-8ba9-400671c48592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:47,258] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:47,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:47,258] [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
Arcticibacterium luteifluviistationis	strain=SM1504	GCA_003258705.1	1784714	1784714	type	True	100.0	1792	1793	95	conclusive
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	75.9925	69	1793	95	below_threshold
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	75.4673	55	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:47,260] [INFO] DFAST Taxonomy check result was written to GCF_003258705.1_ASM325870v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:47,260] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:47,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:47,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge79014c8-8adf-4d98-8ba9-400671c48592/dqc_reference/checkm_data
[2024-01-25 20:12:47,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:47,317] [INFO] Task started: CheckM
[2024-01-25 20:12:47,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258705.1_ASM325870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258705.1_ASM325870v1_genomic.fna/checkm_input GCF_003258705.1_ASM325870v1_genomic.fna/checkm_result
[2024-01-25 20:13:33,345] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:33,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:33,372] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:33,373] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:33,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258705.1_ASM325870v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:33,376] [INFO] Task started: Blastn
[2024-01-25 20:13:33,376] [INFO] Running command: blastn -query GCF_003258705.1_ASM325870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge79014c8-8adf-4d98-8ba9-400671c48592/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258705.1_ASM325870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:34,237] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:34,240] [INFO] Selected 29 target genomes.
[2024-01-25 20:13:34,241] [INFO] Target genome list was writen to GCF_003258705.1_ASM325870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:34,269] [INFO] Task started: fastANI
[2024-01-25 20:13:34,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgc928fa9a-5c9c-4496-9873-4e5b1edf7abc/GCF_003258705.1_ASM325870v1_genomic.fna.gz --refList GCF_003258705.1_ASM325870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258705.1_ASM325870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:57,835] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:57,842] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:57,842] [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_003258705.1	s__Arcticibacterium luteifluviistationis	100.0	1793	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcticibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900230115.1	s__TFI-002 sp900230115	78.2482	166	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__TFI-002	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306455.1	s__Jiulongibacter sediminis	76.6607	122	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Jiulongibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002256295.1	s__Leadbetterella sp002256295	75.7561	71	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	97.02	97.02	0.83	0.83	2	-
GCF_003418935.1	s__Emticicia sp003418935	75.5139	51	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168285.1	s__Emticicia sp004168285	75.4673	55	1793	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	75.3602	55	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:57,844] [INFO] GTDB search result was written to GCF_003258705.1_ASM325870v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:57,845] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:57,849] [INFO] DFAST_QC result json was written to GCF_003258705.1_ASM325870v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:57,849] [INFO] DFAST_QC completed!
[2024-01-25 20:13:57,849] [INFO] Total running time: 0h1m52s