[2024-01-25 19:53:35,537] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg65fa699b-7b45-4bf3-94c3-bb66b76aaeee/dqc_reference
[2024-01-25 19:53:36,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,735] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg287f5289-7f61-44b5-8c4f-2cc18618e589/GCF_002554795.1_ASM255479v1_genomic.fna.gz | prodigal -d GCF_002554795.1_ASM255479v1_genomic.fna/cds.fna -a GCF_002554795.1_ASM255479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:58,282] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:58,282] [INFO] Task started: HMMsearch
[2024-01-25 19:53:58,282] [INFO] Running command: hmmsearch --tblout GCF_002554795.1_ASM255479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65fa699b-7b45-4bf3-94c3-bb66b76aaeee/dqc_reference/reference_markers.hmm GCF_002554795.1_ASM255479v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:58,510] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:58,512] [INFO] Found 6/6 markers.
[2024-01-25 19:53:58,546] [INFO] Query marker FASTA was written to GCF_002554795.1_ASM255479v1_genomic.fna/markers.fasta
[2024-01-25 19:53:58,546] [INFO] Task started: Blastn
[2024-01-25 19:53:58,547] [INFO] Running command: blastn -query GCF_002554795.1_ASM255479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65fa699b-7b45-4bf3-94c3-bb66b76aaeee/dqc_reference/reference_markers.fasta -out GCF_002554795.1_ASM255479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:59,097] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:59,099] [INFO] Selected 24 target genomes.
[2024-01-25 19:53:59,100] [INFO] Target genome list was writen to GCF_002554795.1_ASM255479v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:59,110] [INFO] Task started: fastANI
[2024-01-25 19:53:59,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg287f5289-7f61-44b5-8c4f-2cc18618e589/GCF_002554795.1_ASM255479v1_genomic.fna.gz --refList GCF_002554795.1_ASM255479v1_genomic.fna/target_genomes.txt --output GCF_002554795.1_ASM255479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:13,509] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:13,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65fa699b-7b45-4bf3-94c3-bb66b76aaeee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:13,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65fa699b-7b45-4bf3-94c3-bb66b76aaeee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:13,516] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:13,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:13,516] [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
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	100.0	1457	1459	95	conclusive
Longimonas halophila	strain=KCTC 42399	GCA_002554705.1	1469170	1469170	type	True	76.6429	89	1459	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	76.6034	97	1459	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	76.5294	108	1459	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.1364	66	1459	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	76.0898	107	1459	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	75.5074	68	1459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:13,517] [INFO] DFAST Taxonomy check result was written to GCF_002554795.1_ASM255479v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:13,518] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:13,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:13,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65fa699b-7b45-4bf3-94c3-bb66b76aaeee/dqc_reference/checkm_data
[2024-01-25 19:54:13,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:13,562] [INFO] Task started: CheckM
[2024-01-25 19:54:13,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002554795.1_ASM255479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002554795.1_ASM255479v1_genomic.fna/checkm_input GCF_002554795.1_ASM255479v1_genomic.fna/checkm_result
[2024-01-25 19:55:12,728] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:12,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:12,747] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:12,747] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:12,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002554795.1_ASM255479v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:12,749] [INFO] Task started: Blastn
[2024-01-25 19:55:12,749] [INFO] Running command: blastn -query GCF_002554795.1_ASM255479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65fa699b-7b45-4bf3-94c3-bb66b76aaeee/dqc_reference/reference_markers_gtdb.fasta -out GCF_002554795.1_ASM255479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:13,673] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:13,675] [INFO] Selected 21 target genomes.
[2024-01-25 19:55:13,675] [INFO] Target genome list was writen to GCF_002554795.1_ASM255479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:13,694] [INFO] Task started: fastANI
[2024-01-25 19:55:13,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg287f5289-7f61-44b5-8c4f-2cc18618e589/GCF_002554795.1_ASM255479v1_genomic.fna.gz --refList GCF_002554795.1_ASM255479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002554795.1_ASM255479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:27,733] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:27,742] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:27,742] [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_002554795.1	s__Longibacter salinarum	100.0	1457	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Longibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009908725.1	s__Longibacter sp009908725	79.3924	475	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Longibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002554705.1	s__Longimonas halophila	76.6429	89	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Longimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002894645.1	s__Salinibacter altiplanensis	76.6034	97	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.33	98.12	0.91	0.90	3	-
GCF_000013045.1	s__Salinibacter ruber	76.5294	108	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.51	97.79	0.92	0.85	14	-
GCA_002894685.1	s__Salinibacter luteus	76.4495	124	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCA_003022565.1	s__Salinibacter sp003022565	76.347	80	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954405.1	s__Salinibacter sp002954405	76.1727	82	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908415.1	s__JAAAPH01 sp009908415	76.1581	122	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419585.1	s__Salisaeta longa	76.0898	107	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salisaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908885.1	s__JAAAOL01 sp009908885	75.8828	75	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022435.1	s__Salinibacter sp003022435	75.8313	73	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283365.1	s__Rubrivirga marina	75.5074	68	1459	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:27,743] [INFO] GTDB search result was written to GCF_002554795.1_ASM255479v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:27,744] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:27,746] [INFO] DFAST_QC result json was written to GCF_002554795.1_ASM255479v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:27,746] [INFO] DFAST_QC completed!
[2024-01-25 19:55:27,746] [INFO] Total running time: 0h1m52s