[2023-06-18 18:10:03,681] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:03,684] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:03,684] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6de08d2-2e98-4674-adb8-db63894c42f5/dqc_reference
[2023-06-18 18:10:05,201] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:05,205] [INFO] Task started: Prodigal
[2023-06-18 18:10:05,205] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b0b8f12-6ad5-4841-8a1e-fbbdd89e0357/GCA_018004975.1_ASM1800497v1_genomic.fna.gz | prodigal -d GCA_018004975.1_ASM1800497v1_genomic.fna/cds.fna -a GCA_018004975.1_ASM1800497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:08,086] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:08,087] [INFO] Task started: HMMsearch
[2023-06-18 18:10:08,087] [INFO] Running command: hmmsearch --tblout GCA_018004975.1_ASM1800497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6de08d2-2e98-4674-adb8-db63894c42f5/dqc_reference/reference_markers.hmm GCA_018004975.1_ASM1800497v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:08,274] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:08,275] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1b0b8f12-6ad5-4841-8a1e-fbbdd89e0357/GCA_018004975.1_ASM1800497v1_genomic.fna.gz]
[2023-06-18 18:10:08,293] [INFO] Query marker FASTA was written to GCA_018004975.1_ASM1800497v1_genomic.fna/markers.fasta
[2023-06-18 18:10:08,293] [INFO] Task started: Blastn
[2023-06-18 18:10:08,293] [INFO] Running command: blastn -query GCA_018004975.1_ASM1800497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6de08d2-2e98-4674-adb8-db63894c42f5/dqc_reference/reference_markers.fasta -out GCA_018004975.1_ASM1800497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:08,847] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:08,852] [INFO] Selected 11 target genomes.
[2023-06-18 18:10:08,853] [INFO] Target genome list was writen to GCA_018004975.1_ASM1800497v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:08,855] [INFO] Task started: fastANI
[2023-06-18 18:10:08,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0b8f12-6ad5-4841-8a1e-fbbdd89e0357/GCA_018004975.1_ASM1800497v1_genomic.fna.gz --refList GCA_018004975.1_ASM1800497v1_genomic.fna/target_genomes.txt --output GCA_018004975.1_ASM1800497v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:14,276] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:14,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6de08d2-2e98-4674-adb8-db63894c42f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:14,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6de08d2-2e98-4674-adb8-db63894c42f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:14,285] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:14,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:10:14,285] [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
Cloacibacterium rupense	strain=CGMCC 1.7656	GCA_014645495.1	517423	517423	type	True	87.0215	157	188	95	below_threshold
Cloacibacterium normanense	strain=NRS-1	GCA_001747495.1	237258	237258	type	True	81.6059	128	188	95	below_threshold
Cloacibacterium normanense	strain=DSM 15886	GCA_900104195.1	237258	237258	type	True	81.5851	130	188	95	below_threshold
Cloacibacterium normanense	strain=NRS-1	GCA_003860565.1	237258	237258	type	True	81.5172	130	188	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:10:14,288] [INFO] DFAST Taxonomy check result was written to GCA_018004975.1_ASM1800497v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:14,289] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:14,289] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:14,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6de08d2-2e98-4674-adb8-db63894c42f5/dqc_reference/checkm_data
[2023-06-18 18:10:14,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:14,312] [INFO] Task started: CheckM
[2023-06-18 18:10:14,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018004975.1_ASM1800497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018004975.1_ASM1800497v1_genomic.fna/checkm_input GCA_018004975.1_ASM1800497v1_genomic.fna/checkm_result
[2023-06-18 18:10:30,772] [INFO] Task succeeded: CheckM
[2023-06-18 18:10:30,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:10:30,806] [INFO] ===== Completeness check finished =====
[2023-06-18 18:10:30,806] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:10:30,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018004975.1_ASM1800497v1_genomic.fna/markers.fasta)
[2023-06-18 18:10:30,807] [INFO] Task started: Blastn
[2023-06-18 18:10:30,807] [INFO] Running command: blastn -query GCA_018004975.1_ASM1800497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6de08d2-2e98-4674-adb8-db63894c42f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_018004975.1_ASM1800497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:31,494] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:31,498] [INFO] Selected 7 target genomes.
[2023-06-18 18:10:31,499] [INFO] Target genome list was writen to GCA_018004975.1_ASM1800497v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:10:31,502] [INFO] Task started: fastANI
[2023-06-18 18:10:31,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0b8f12-6ad5-4841-8a1e-fbbdd89e0357/GCA_018004975.1_ASM1800497v1_genomic.fna.gz --refList GCA_018004975.1_ASM1800497v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018004975.1_ASM1800497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:10:34,752] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:34,760] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 18:10:34,760] [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
GCA_002337005.1	s__Cloacibacterium sp002337005	92.5536	157	188	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645495.1	s__Cloacibacterium rupense	87.0215	157	188	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860565.1	s__Cloacibacterium normanense	81.5172	130	188	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	98.41	95.23	0.95	0.87	4	-
GCF_907163125.1	s__Cloacibacterium caeni_B	81.4817	131	188	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCF_907163105.1	s__Cloacibacterium caeni_A	81.4784	134	188	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943105.1	s__Cloacibacterium sp002422665	81.2079	125	188	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0662	95.27	95.25	0.87	0.85	3	-
GCF_900108025.1	s__Halpernia humi	76.429	55	188	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Halpernia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:10:34,762] [INFO] GTDB search result was written to GCA_018004975.1_ASM1800497v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:10:34,762] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:10:34,765] [INFO] DFAST_QC result json was written to GCA_018004975.1_ASM1800497v1_genomic.fna/dqc_result.json
[2023-06-18 18:10:34,765] [INFO] DFAST_QC completed!
[2023-06-18 18:10:34,765] [INFO] Total running time: 0h0m31s