[2023-06-16 21:40:33,394] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:40:33,397] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:40:33,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg8da8d5a7-a103-4bf5-bddc-216db8161a97/dqc_reference
[2023-06-16 21:40:34,695] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:40:34,696] [INFO] Task started: Prodigal
[2023-06-16 21:40:34,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f03fd7e-d205-4873-95dd-2183905a32f7/GCA_028067765.1_ASM2806776v1_genomic.fna.gz | prodigal -d GCA_028067765.1_ASM2806776v1_genomic.fna/cds.fna -a GCA_028067765.1_ASM2806776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:40:46,720] [INFO] Task succeeded: Prodigal
[2023-06-16 21:40:46,720] [INFO] Task started: HMMsearch
[2023-06-16 21:40:46,720] [INFO] Running command: hmmsearch --tblout GCA_028067765.1_ASM2806776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8da8d5a7-a103-4bf5-bddc-216db8161a97/dqc_reference/reference_markers.hmm GCA_028067765.1_ASM2806776v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:40:47,025] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:40:47,026] [INFO] Found 6/6 markers.
[2023-06-16 21:40:47,069] [INFO] Query marker FASTA was written to GCA_028067765.1_ASM2806776v1_genomic.fna/markers.fasta
[2023-06-16 21:40:47,069] [INFO] Task started: Blastn
[2023-06-16 21:40:47,070] [INFO] Running command: blastn -query GCA_028067765.1_ASM2806776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8da8d5a7-a103-4bf5-bddc-216db8161a97/dqc_reference/reference_markers.fasta -out GCA_028067765.1_ASM2806776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:40:47,766] [INFO] Task succeeded: Blastn
[2023-06-16 21:40:47,771] [INFO] Selected 28 target genomes.
[2023-06-16 21:40:47,771] [INFO] Target genome list was writen to GCA_028067765.1_ASM2806776v1_genomic.fna/target_genomes.txt
[2023-06-16 21:40:47,777] [INFO] Task started: fastANI
[2023-06-16 21:40:47,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f03fd7e-d205-4873-95dd-2183905a32f7/GCA_028067765.1_ASM2806776v1_genomic.fna.gz --refList GCA_028067765.1_ASM2806776v1_genomic.fna/target_genomes.txt --output GCA_028067765.1_ASM2806776v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:41:11,371] [INFO] Task succeeded: fastANI
[2023-06-16 21:41:11,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8da8d5a7-a103-4bf5-bddc-216db8161a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:41:11,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8da8d5a7-a103-4bf5-bddc-216db8161a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:41:11,400] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:41:11,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 21:41:11,400] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.0052	93	1303	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.8446	175	1303	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.82	154	1303	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.4293	189	1303	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	75.2526	96	1303	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	75.2265	118	1303	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	75.2008	124	1303	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	75.1945	125	1303	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	75.0722	187	1303	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	75.0396	142	1303	95	below_threshold
Rhodococcus corynebacterioides	strain=NBRC 14404	GCA_001894765.1	53972	53972	suspected-type	True	75.0336	74	1303	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	75.0246	198	1303	95	below_threshold
Catenulispora acidiphila	strain=DSM 44928	GCA_000024025.1	304895	304895	type	True	75.0227	140	1303	95	below_threshold
Goekera deserti	strain=CPCC 205119	GCA_010685995.1	2497753	2497753	type	True	75.013	134	1303	95	below_threshold
Saccharopolyspora gloriosae	strain=DSM 45582	GCA_014203325.1	455344	455344	type	True	74.988	111	1303	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.9847	194	1303	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	74.9521	96	1303	95	below_threshold
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	74.8924	126	1303	95	below_threshold
Bifidobacterium italicum	strain=Rab10A	GCA_002286915.1	1960968	1960968	type	True	74.89	54	1303	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	74.8725	77	1303	95	below_threshold
Tenggerimyces flavus	strain=DSM 28944	GCA_016907715.1	1708749	1708749	type	True	74.8656	149	1303	95	below_threshold
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	74.848	121	1303	95	below_threshold
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	74.8374	162	1303	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 21:41:11,402] [INFO] DFAST Taxonomy check result was written to GCA_028067765.1_ASM2806776v1_genomic.fna/tc_result.tsv
[2023-06-16 21:41:11,403] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:41:11,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:41:11,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8da8d5a7-a103-4bf5-bddc-216db8161a97/dqc_reference/checkm_data
[2023-06-16 21:41:11,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:41:11,449] [INFO] Task started: CheckM
[2023-06-16 21:41:11,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028067765.1_ASM2806776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028067765.1_ASM2806776v1_genomic.fna/checkm_input GCA_028067765.1_ASM2806776v1_genomic.fna/checkm_result
[2023-06-16 21:41:55,157] [INFO] Task succeeded: CheckM
[2023-06-16 21:41:55,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:41:55,182] [INFO] ===== Completeness check finished =====
[2023-06-16 21:41:55,183] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:41:55,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028067765.1_ASM2806776v1_genomic.fna/markers.fasta)
[2023-06-16 21:41:55,184] [INFO] Task started: Blastn
[2023-06-16 21:41:55,184] [INFO] Running command: blastn -query GCA_028067765.1_ASM2806776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8da8d5a7-a103-4bf5-bddc-216db8161a97/dqc_reference/reference_markers_gtdb.fasta -out GCA_028067765.1_ASM2806776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:41:56,143] [INFO] Task succeeded: Blastn
[2023-06-16 21:41:56,147] [INFO] Selected 25 target genomes.
[2023-06-16 21:41:56,147] [INFO] Target genome list was writen to GCA_028067765.1_ASM2806776v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:41:56,155] [INFO] Task started: fastANI
[2023-06-16 21:41:56,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f03fd7e-d205-4873-95dd-2183905a32f7/GCA_028067765.1_ASM2806776v1_genomic.fna.gz --refList GCA_028067765.1_ASM2806776v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028067765.1_ASM2806776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:42:09,588] [INFO] Task succeeded: fastANI
[2023-06-16 21:42:09,609] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 21:42:09,609] [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_003155135.1	s__Bog-515 sp003155135	77.3202	188	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
GCA_003151235.1	s__Palsa-461 sp003151235	77.1277	164	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-461	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478655.1	s__Bog-756 sp015478655	77.0405	115	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164095.1	s__Bog-756 sp003164095	76.9506	139	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161575.1	s__PALSA-457 sp003161575	76.9122	147	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__PALSA-457	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161255.1	s__Palsa-461 sp003161255	76.873	157	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-461	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138855.1	s__Bog-756 sp003138855	76.705	133	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.82	99.61	0.95	0.93	14	-
GCA_017882995.1	s__Chersky-840 sp017882995	76.5898	120	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__Chersky-840	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894295.1	s__Bog-756 sp903894295	76.567	76	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.67	99.55	0.93	0.92	5	-
GCA_003453695.1	s__UBA8190 sp003453695	76.5269	129	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__UBA8190	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169235.1	s__Bog-473 sp003169235	76.5145	147	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-473	95.0	99.17	99.17	0.82	0.82	2	-
GCA_017883065.1	s__Bog-756 sp017883065	76.4356	123	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151955.1	s__PALSA-743 sp003151955	76.3613	144	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__PALSA-743	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.1507	180	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133665.1	s__RAAP-2 sp003133665	75.9736	68	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888295.1	s__AC-9 sp005888295	75.9357	151	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__QHCF01;g__AC-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884125.1	s__AC-35 sp005884125	75.9149	118	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-35;g__AC-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	75.6516	114	1303	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873275.1	s__VGXO01 sp016873275	74.7807	88	1303	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__VGXO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873255.1	s__UBA966 sp016873255	74.7337	60	1303	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 21:42:09,612] [INFO] GTDB search result was written to GCA_028067765.1_ASM2806776v1_genomic.fna/result_gtdb.tsv
[2023-06-16 21:42:09,613] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:42:09,618] [INFO] DFAST_QC result json was written to GCA_028067765.1_ASM2806776v1_genomic.fna/dqc_result.json
[2023-06-16 21:42:09,618] [INFO] DFAST_QC completed!
[2023-06-16 21:42:09,618] [INFO] Total running time: 0h1m36s