[2024-01-24 11:51:06,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg356ddd8f-bc7b-4385-83eb-c7e9c9a57d43/dqc_reference
[2024-01-24 11:51:08,270] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,271] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,271] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa49d727-3810-4699-bbc4-e228857b1ed4/GCF_003001895.1_ASM300189v1_genomic.fna.gz | prodigal -d GCF_003001895.1_ASM300189v1_genomic.fna/cds.fna -a GCF_003001895.1_ASM300189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:20,671] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:20,671] [INFO] Task started: HMMsearch
[2024-01-24 11:51:20,672] [INFO] Running command: hmmsearch --tblout GCF_003001895.1_ASM300189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg356ddd8f-bc7b-4385-83eb-c7e9c9a57d43/dqc_reference/reference_markers.hmm GCF_003001895.1_ASM300189v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:21,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:21,022] [INFO] Found 6/6 markers.
[2024-01-24 11:51:21,058] [INFO] Query marker FASTA was written to GCF_003001895.1_ASM300189v1_genomic.fna/markers.fasta
[2024-01-24 11:51:21,058] [INFO] Task started: Blastn
[2024-01-24 11:51:21,058] [INFO] Running command: blastn -query GCF_003001895.1_ASM300189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg356ddd8f-bc7b-4385-83eb-c7e9c9a57d43/dqc_reference/reference_markers.fasta -out GCF_003001895.1_ASM300189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:21,714] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:21,720] [INFO] Selected 12 target genomes.
[2024-01-24 11:51:21,720] [INFO] Target genome list was writen to GCF_003001895.1_ASM300189v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:21,727] [INFO] Task started: fastANI
[2024-01-24 11:51:21,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa49d727-3810-4699-bbc4-e228857b1ed4/GCF_003001895.1_ASM300189v1_genomic.fna.gz --refList GCF_003001895.1_ASM300189v1_genomic.fna/target_genomes.txt --output GCF_003001895.1_ASM300189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:32,062] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:32,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg356ddd8f-bc7b-4385-83eb-c7e9c9a57d43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:32,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg356ddd8f-bc7b-4385-83eb-c7e9c9a57d43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:32,077] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:32,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:32,078] [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 salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	99.9982	1233	1239	95	conclusive
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	99.9897	1238	1239	95	conclusive
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	88.0144	1015	1239	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	86.9451	974	1239	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	86.1	912	1239	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	85.1503	875	1239	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	85.1483	883	1239	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	84.7873	853	1239	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	84.3433	841	1239	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	77.4586	196	1239	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.5109	71	1239	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.4016	97	1239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:32,080] [INFO] DFAST Taxonomy check result was written to GCF_003001895.1_ASM300189v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:32,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:32,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:32,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg356ddd8f-bc7b-4385-83eb-c7e9c9a57d43/dqc_reference/checkm_data
[2024-01-24 11:51:32,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:32,119] [INFO] Task started: CheckM
[2024-01-24 11:51:32,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003001895.1_ASM300189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003001895.1_ASM300189v1_genomic.fna/checkm_input GCF_003001895.1_ASM300189v1_genomic.fna/checkm_result
[2024-01-24 11:52:11,993] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:11,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:12,018] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:12,019] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:12,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003001895.1_ASM300189v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:12,020] [INFO] Task started: Blastn
[2024-01-24 11:52:12,020] [INFO] Running command: blastn -query GCF_003001895.1_ASM300189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg356ddd8f-bc7b-4385-83eb-c7e9c9a57d43/dqc_reference/reference_markers_gtdb.fasta -out GCF_003001895.1_ASM300189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:12,871] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:12,876] [INFO] Selected 7 target genomes.
[2024-01-24 11:52:12,876] [INFO] Target genome list was writen to GCF_003001895.1_ASM300189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:12,882] [INFO] Task started: fastANI
[2024-01-24 11:52:12,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa49d727-3810-4699-bbc4-e228857b1ed4/GCF_003001895.1_ASM300189v1_genomic.fna.gz --refList GCF_003001895.1_ASM300189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003001895.1_ASM300189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:19,809] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:19,816] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:19,816] [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_900142975.1	s__Salegentibacter salegens	99.9897	1238	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900113135.1	s__Salegentibacter agarivorans	87.9871	1017	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900168115.1	s__Salegentibacter salinarum	86.9193	987	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900168265.1	s__Salegentibacter salarius	85.5213	850	1239	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	85.1512	883	1239	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	84.8425	895	1239	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	84.3397	842	1239	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 11:52:19,818] [INFO] GTDB search result was written to GCF_003001895.1_ASM300189v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:19,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:19,822] [INFO] DFAST_QC result json was written to GCF_003001895.1_ASM300189v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:19,822] [INFO] DFAST_QC completed!
[2024-01-24 11:52:19,822] [INFO] Total running time: 0h1m13s