[2023-06-19 06:19:45,765] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:19:45,767] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:19:45,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg20d4fc33-7ae0-4e88-94c8-387fd5a98e67/dqc_reference
[2023-06-19 06:19:47,220] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:19:47,221] [INFO] Task started: Prodigal
[2023-06-19 06:19:47,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ab10596-5e65-4072-9312-cb46bd925154/GCA_013697635.1_ASM1369763v1_genomic.fna.gz | prodigal -d GCA_013697635.1_ASM1369763v1_genomic.fna/cds.fna -a GCA_013697635.1_ASM1369763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:20:06,420] [INFO] Task succeeded: Prodigal
[2023-06-19 06:20:06,421] [INFO] Task started: HMMsearch
[2023-06-19 06:20:06,421] [INFO] Running command: hmmsearch --tblout GCA_013697635.1_ASM1369763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20d4fc33-7ae0-4e88-94c8-387fd5a98e67/dqc_reference/reference_markers.hmm GCA_013697635.1_ASM1369763v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:20:06,778] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:20:06,780] [INFO] Found 6/6 markers.
[2023-06-19 06:20:06,832] [INFO] Query marker FASTA was written to GCA_013697635.1_ASM1369763v1_genomic.fna/markers.fasta
[2023-06-19 06:20:06,833] [INFO] Task started: Blastn
[2023-06-19 06:20:06,833] [INFO] Running command: blastn -query GCA_013697635.1_ASM1369763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d4fc33-7ae0-4e88-94c8-387fd5a98e67/dqc_reference/reference_markers.fasta -out GCA_013697635.1_ASM1369763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:20:07,626] [INFO] Task succeeded: Blastn
[2023-06-19 06:20:07,635] [INFO] Selected 20 target genomes.
[2023-06-19 06:20:07,636] [INFO] Target genome list was writen to GCA_013697635.1_ASM1369763v1_genomic.fna/target_genomes.txt
[2023-06-19 06:20:07,639] [INFO] Task started: fastANI
[2023-06-19 06:20:07,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab10596-5e65-4072-9312-cb46bd925154/GCA_013697635.1_ASM1369763v1_genomic.fna.gz --refList GCA_013697635.1_ASM1369763v1_genomic.fna/target_genomes.txt --output GCA_013697635.1_ASM1369763v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:20:22,585] [INFO] Task succeeded: fastANI
[2023-06-19 06:20:22,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20d4fc33-7ae0-4e88-94c8-387fd5a98e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:20:22,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20d4fc33-7ae0-4e88-94c8-387fd5a98e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:20:22,596] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:20:22,596] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:20:22,596] [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
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	77.0182	336	1963	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	76.8847	253	1963	95	below_threshold
Lujinxingia sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	76.6882	271	1963	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	76.6373	343	1963	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	76.6369	343	1963	95	below_threshold
Desulfarculus baarsii	strain=DSM 2075	GCA_000143965.1	453230	453230	type	True	75.1946	67	1963	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	75.1647	52	1963	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1417	121	1963	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	74.9413	104	1963	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	74.913	86	1963	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	74.7342	91	1963	95	below_threshold
Phytoactinopolyspora mesophila	strain=XMNu-373	GCA_010122465.1	2650750	2650750	type	True	74.5653	52	1963	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:20:22,598] [INFO] DFAST Taxonomy check result was written to GCA_013697635.1_ASM1369763v1_genomic.fna/tc_result.tsv
[2023-06-19 06:20:22,599] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:20:22,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:20:22,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20d4fc33-7ae0-4e88-94c8-387fd5a98e67/dqc_reference/checkm_data
[2023-06-19 06:20:22,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:20:22,666] [INFO] Task started: CheckM
[2023-06-19 06:20:22,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013697635.1_ASM1369763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013697635.1_ASM1369763v1_genomic.fna/checkm_input GCA_013697635.1_ASM1369763v1_genomic.fna/checkm_result
[2023-06-19 06:21:19,007] [INFO] Task succeeded: CheckM
[2023-06-19 06:21:19,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:21:19,039] [INFO] ===== Completeness check finished =====
[2023-06-19 06:21:19,039] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:21:19,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013697635.1_ASM1369763v1_genomic.fna/markers.fasta)
[2023-06-19 06:21:19,040] [INFO] Task started: Blastn
[2023-06-19 06:21:19,040] [INFO] Running command: blastn -query GCA_013697635.1_ASM1369763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d4fc33-7ae0-4e88-94c8-387fd5a98e67/dqc_reference/reference_markers_gtdb.fasta -out GCA_013697635.1_ASM1369763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:21:20,261] [INFO] Task succeeded: Blastn
[2023-06-19 06:21:20,268] [INFO] Selected 19 target genomes.
[2023-06-19 06:21:20,268] [INFO] Target genome list was writen to GCA_013697635.1_ASM1369763v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:21:20,335] [INFO] Task started: fastANI
[2023-06-19 06:21:20,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab10596-5e65-4072-9312-cb46bd925154/GCA_013697635.1_ASM1369763v1_genomic.fna.gz --refList GCA_013697635.1_ASM1369763v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013697635.1_ASM1369763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:21:34,051] [INFO] Task succeeded: fastANI
[2023-06-19 06:21:34,072] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:21:34,073] [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_013697635.1	s__JACCWM01 sp013697635	100.0	1951	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007997015.1	s__Lujinxingia sp007997015	77.0101	337	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007997005.1	s__Lujinxingia sp007997005	76.923	309	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260125.1	s__Lujinxingia litoralis	76.895	252	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005565.1	s__Lujinxingia sediminis	76.6799	272	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	-
GCF_006517175.1	s__Persicimonas caeni	76.6364	343	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007135085.1	s__SLJM01 sp007135085	75.8937	159	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SLJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859985.1	s__LZORAL124-64-63 sp014859985	75.3175	64	1963	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__LZORAL124-64-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119595.1	s__SLJM01 sp007119595	75.261	72	1963	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SLJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	75.0736	62	1963	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCA_016709665.1	s__FEB-7 sp016709665	75.0721	77	1963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879205.1	s__DP-3 sp005879205	74.8541	55	1963	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:21:34,081] [INFO] GTDB search result was written to GCA_013697635.1_ASM1369763v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:21:34,082] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:21:34,093] [INFO] DFAST_QC result json was written to GCA_013697635.1_ASM1369763v1_genomic.fna/dqc_result.json
[2023-06-19 06:21:34,093] [INFO] DFAST_QC completed!
[2023-06-19 06:21:34,094] [INFO] Total running time: 0h1m48s