[2024-01-25 19:58:50,901] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:50,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:50,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f6e2eb3-7235-4114-a429-4fdb9b892f54/dqc_reference
[2024-01-25 19:58:52,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:52,127] [INFO] Task started: Prodigal
[2024-01-25 19:58:52,127] [INFO] Running command: gunzip -c /var/lib/cwl/stga4153434-d050-49cb-a6c5-e3bf1334bdfa/GCF_014644295.1_ASM1464429v1_genomic.fna.gz | prodigal -d GCF_014644295.1_ASM1464429v1_genomic.fna/cds.fna -a GCF_014644295.1_ASM1464429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:16,492] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:16,492] [INFO] Task started: HMMsearch
[2024-01-25 19:59:16,493] [INFO] Running command: hmmsearch --tblout GCF_014644295.1_ASM1464429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f6e2eb3-7235-4114-a429-4fdb9b892f54/dqc_reference/reference_markers.hmm GCF_014644295.1_ASM1464429v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:16,843] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:16,844] [INFO] Found 6/6 markers.
[2024-01-25 19:59:16,895] [INFO] Query marker FASTA was written to GCF_014644295.1_ASM1464429v1_genomic.fna/markers.fasta
[2024-01-25 19:59:16,896] [INFO] Task started: Blastn
[2024-01-25 19:59:16,896] [INFO] Running command: blastn -query GCF_014644295.1_ASM1464429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6e2eb3-7235-4114-a429-4fdb9b892f54/dqc_reference/reference_markers.fasta -out GCF_014644295.1_ASM1464429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:17,447] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:17,450] [INFO] Selected 20 target genomes.
[2024-01-25 19:59:17,450] [INFO] Target genome list was writen to GCF_014644295.1_ASM1464429v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:17,483] [INFO] Task started: fastANI
[2024-01-25 19:59:17,484] [INFO] Running command: fastANI --query /var/lib/cwl/stga4153434-d050-49cb-a6c5-e3bf1334bdfa/GCF_014644295.1_ASM1464429v1_genomic.fna.gz --refList GCF_014644295.1_ASM1464429v1_genomic.fna/target_genomes.txt --output GCF_014644295.1_ASM1464429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:34,165] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:34,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f6e2eb3-7235-4114-a429-4fdb9b892f54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:34,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f6e2eb3-7235-4114-a429-4fdb9b892f54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:34,172] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:34,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:34,172] [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 aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	100.0	2234	2234	95	conclusive
Emticicia aquatica	strain=CECT 8858, type strain	GCA_923079645.1	1681835	1681835	type	True	79.8781	960	2234	95	below_threshold
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	78.0195	133	2234	95	below_threshold
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	76.7167	297	2234	95	below_threshold
Arcicella aurantiaca	strain=DSM 22214	GCA_003148625.1	591202	591202	type	True	76.4917	215	2234	95	below_threshold
Flectobacillus major	strain=DSM 103	GCA_000427405.1	103	103	type	True	76.272	136	2234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:34,176] [INFO] DFAST Taxonomy check result was written to GCF_014644295.1_ASM1464429v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:34,177] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:34,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:34,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f6e2eb3-7235-4114-a429-4fdb9b892f54/dqc_reference/checkm_data
[2024-01-25 19:59:34,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:34,239] [INFO] Task started: CheckM
[2024-01-25 19:59:34,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644295.1_ASM1464429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644295.1_ASM1464429v1_genomic.fna/checkm_input GCF_014644295.1_ASM1464429v1_genomic.fna/checkm_result
[2024-01-25 20:00:41,957] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:41,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:41,991] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:41,991] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:41,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644295.1_ASM1464429v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:41,993] [INFO] Task started: Blastn
[2024-01-25 20:00:41,993] [INFO] Running command: blastn -query GCF_014644295.1_ASM1464429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6e2eb3-7235-4114-a429-4fdb9b892f54/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644295.1_ASM1464429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:42,787] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:42,789] [INFO] Selected 15 target genomes.
[2024-01-25 20:00:42,790] [INFO] Target genome list was writen to GCF_014644295.1_ASM1464429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:42,806] [INFO] Task started: fastANI
[2024-01-25 20:00:42,806] [INFO] Running command: fastANI --query /var/lib/cwl/stga4153434-d050-49cb-a6c5-e3bf1334bdfa/GCF_014644295.1_ASM1464429v1_genomic.fna.gz --refList GCF_014644295.1_ASM1464429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644295.1_ASM1464429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:00,131] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:00,139] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:00,139] [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_014644295.1	s__Emticicia aquatilis	100.0	2234	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017495105.1	s__Emticicia sp017495105	84.2047	1095	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000263195.1	s__Emticicia oligotrophica	80.3301	1035	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855535.1	s__Emticicia sp002855535	76.855	176	2234	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	76.8106	304	2234	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	76.7924	265	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148625.1	s__Arcicella aurantiaca	76.5002	214	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256295.1	s__Leadbetterella sp002256295	76.3421	97	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	97.02	97.02	0.83	0.83	2	-
GCA_016722655.1	s__Leadbetterella sp016722655	76.0806	85	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	99.38	99.07	0.96	0.94	5	-
GCA_014376355.1	s__Arcicella sp014376355	75.9934	94	2234	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	75.7074	121	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:00,140] [INFO] GTDB search result was written to GCF_014644295.1_ASM1464429v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:00,141] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:00,143] [INFO] DFAST_QC result json was written to GCF_014644295.1_ASM1464429v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:00,143] [INFO] DFAST_QC completed!
[2024-01-25 20:01:00,143] [INFO] Total running time: 0h2m9s