[2024-01-24 13:36:45,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dec03f8-f3ba-48b6-aeb7-f1456e39a06a/dqc_reference
[2024-01-24 13:36:47,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,082] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgda5007d9-d318-426a-919e-224e25598a33/GCF_020164555.1_ASM2016455v1_genomic.fna.gz | prodigal -d GCF_020164555.1_ASM2016455v1_genomic.fna/cds.fna -a GCF_020164555.1_ASM2016455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:00,228] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:00,229] [INFO] Task started: HMMsearch
[2024-01-24 13:37:00,229] [INFO] Running command: hmmsearch --tblout GCF_020164555.1_ASM2016455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dec03f8-f3ba-48b6-aeb7-f1456e39a06a/dqc_reference/reference_markers.hmm GCF_020164555.1_ASM2016455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:00,473] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:00,475] [INFO] Found 6/6 markers.
[2024-01-24 13:37:00,506] [INFO] Query marker FASTA was written to GCF_020164555.1_ASM2016455v1_genomic.fna/markers.fasta
[2024-01-24 13:37:00,507] [INFO] Task started: Blastn
[2024-01-24 13:37:00,507] [INFO] Running command: blastn -query GCF_020164555.1_ASM2016455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dec03f8-f3ba-48b6-aeb7-f1456e39a06a/dqc_reference/reference_markers.fasta -out GCF_020164555.1_ASM2016455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:01,207] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:01,210] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:01,210] [INFO] Target genome list was writen to GCF_020164555.1_ASM2016455v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:01,215] [INFO] Task started: fastANI
[2024-01-24 13:37:01,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgda5007d9-d318-426a-919e-224e25598a33/GCF_020164555.1_ASM2016455v1_genomic.fna.gz --refList GCF_020164555.1_ASM2016455v1_genomic.fna/target_genomes.txt --output GCF_020164555.1_ASM2016455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:11,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:11,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dec03f8-f3ba-48b6-aeb7-f1456e39a06a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:11,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dec03f8-f3ba-48b6-aeb7-f1456e39a06a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:11,264] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:11,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:11,264] [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
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	100.0	1310	1312	95	conclusive
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	86.6833	961	1312	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	86.6497	914	1312	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	86.6338	987	1312	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	86.1527	918	1312	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	86.0303	937	1312	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	85.9846	946	1312	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	85.4655	863	1312	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	85.4469	859	1312	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	77.1517	209	1312	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2451	88	1312	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.0635	70	1312	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:11,266] [INFO] DFAST Taxonomy check result was written to GCF_020164555.1_ASM2016455v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:11,266] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:11,266] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:11,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dec03f8-f3ba-48b6-aeb7-f1456e39a06a/dqc_reference/checkm_data
[2024-01-24 13:37:11,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:11,308] [INFO] Task started: CheckM
[2024-01-24 13:37:11,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020164555.1_ASM2016455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020164555.1_ASM2016455v1_genomic.fna/checkm_input GCF_020164555.1_ASM2016455v1_genomic.fna/checkm_result
[2024-01-24 13:37:54,365] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:54,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:54,390] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:54,390] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:54,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020164555.1_ASM2016455v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:54,391] [INFO] Task started: Blastn
[2024-01-24 13:37:54,391] [INFO] Running command: blastn -query GCF_020164555.1_ASM2016455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dec03f8-f3ba-48b6-aeb7-f1456e39a06a/dqc_reference/reference_markers_gtdb.fasta -out GCF_020164555.1_ASM2016455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:55,496] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:55,499] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:55,499] [INFO] Target genome list was writen to GCF_020164555.1_ASM2016455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:55,517] [INFO] Task started: fastANI
[2024-01-24 13:37:55,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgda5007d9-d318-426a-919e-224e25598a33/GCF_020164555.1_ASM2016455v1_genomic.fna.gz --refList GCF_020164555.1_ASM2016455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020164555.1_ASM2016455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:02,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:02,252] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:02,252] [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_900168115.1	s__Salegentibacter salinarum	86.6957	960	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142975.1	s__Salegentibacter salegens	86.0303	938	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900113135.1	s__Salegentibacter agarivorans	86.0015	945	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900168265.1	s__Salegentibacter salarius	85.475	861	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_002900095.1	s__Salegentibacter mishustinae	84.3252	867	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_000745315.1	s__Salegentibacter sp000745315	83.8899	906	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	83.2338	826	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:02,254] [INFO] GTDB search result was written to GCF_020164555.1_ASM2016455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:02,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:02,258] [INFO] DFAST_QC result json was written to GCF_020164555.1_ASM2016455v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:02,258] [INFO] DFAST_QC completed!
[2024-01-24 13:38:02,258] [INFO] Total running time: 0h1m17s