[2023-06-16 23:43:39,319] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:43:39,323] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:43:39,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg35265e95-95d7-4e32-9996-7928e8cb64db/dqc_reference
[2023-06-16 23:43:40,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:43:40,781] [INFO] Task started: Prodigal
[2023-06-16 23:43:40,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg132c639f-b6ea-4209-bfab-53977d474642/GCA_028063585.1_ASM2806358v1_genomic.fna.gz | prodigal -d GCA_028063585.1_ASM2806358v1_genomic.fna/cds.fna -a GCA_028063585.1_ASM2806358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:43:48,536] [INFO] Task succeeded: Prodigal
[2023-06-16 23:43:48,537] [INFO] Task started: HMMsearch
[2023-06-16 23:43:48,537] [INFO] Running command: hmmsearch --tblout GCA_028063585.1_ASM2806358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35265e95-95d7-4e32-9996-7928e8cb64db/dqc_reference/reference_markers.hmm GCA_028063585.1_ASM2806358v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:43:48,812] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:43:48,814] [INFO] Found 6/6 markers.
[2023-06-16 23:43:48,856] [INFO] Query marker FASTA was written to GCA_028063585.1_ASM2806358v1_genomic.fna/markers.fasta
[2023-06-16 23:43:48,857] [INFO] Task started: Blastn
[2023-06-16 23:43:48,857] [INFO] Running command: blastn -query GCA_028063585.1_ASM2806358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35265e95-95d7-4e32-9996-7928e8cb64db/dqc_reference/reference_markers.fasta -out GCA_028063585.1_ASM2806358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:43:49,699] [INFO] Task succeeded: Blastn
[2023-06-16 23:43:49,703] [INFO] Selected 21 target genomes.
[2023-06-16 23:43:49,704] [INFO] Target genome list was writen to GCA_028063585.1_ASM2806358v1_genomic.fna/target_genomes.txt
[2023-06-16 23:43:49,709] [INFO] Task started: fastANI
[2023-06-16 23:43:49,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg132c639f-b6ea-4209-bfab-53977d474642/GCA_028063585.1_ASM2806358v1_genomic.fna.gz --refList GCA_028063585.1_ASM2806358v1_genomic.fna/target_genomes.txt --output GCA_028063585.1_ASM2806358v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:44:09,109] [INFO] Task succeeded: fastANI
[2023-06-16 23:44:09,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35265e95-95d7-4e32-9996-7928e8cb64db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:44:09,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35265e95-95d7-4e32-9996-7928e8cb64db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:44:09,126] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:44:09,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 23:44:09,126] [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	76.2687	137	925	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.2646	244	925	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.0257	230	925	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.6656	250	925	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.5722	170	925	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	75.3676	213	925	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	75.3363	188	925	95	below_threshold
Tessaracoccus bendigoensis	strain=DSM 12906	GCA_900141915.1	72764	72764	type	True	75.3345	62	925	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	75.3176	149	925	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	75.2596	181	925	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	75.2394	142	925	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	75.2226	176	925	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	75.2162	189	925	95	below_threshold
Pseudonocardia sediminis	strain=DSM 45779	GCA_004217185.1	1397368	1397368	type	True	75.1503	236	925	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	75.0948	188	925	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.072	272	925	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	75.0164	274	925	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	74.9664	249	925	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	74.9209	248	925	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	74.7738	118	925	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 23:44:09,129] [INFO] DFAST Taxonomy check result was written to GCA_028063585.1_ASM2806358v1_genomic.fna/tc_result.tsv
[2023-06-16 23:44:09,129] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:44:09,129] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:44:09,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35265e95-95d7-4e32-9996-7928e8cb64db/dqc_reference/checkm_data
[2023-06-16 23:44:09,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:44:09,190] [INFO] Task started: CheckM
[2023-06-16 23:44:09,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028063585.1_ASM2806358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028063585.1_ASM2806358v1_genomic.fna/checkm_input GCA_028063585.1_ASM2806358v1_genomic.fna/checkm_result
[2023-06-16 23:44:38,050] [INFO] Task succeeded: CheckM
[2023-06-16 23:44:38,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.90%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 23:44:38,079] [INFO] ===== Completeness check finished =====
[2023-06-16 23:44:38,079] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:44:38,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028063585.1_ASM2806358v1_genomic.fna/markers.fasta)
[2023-06-16 23:44:38,080] [INFO] Task started: Blastn
[2023-06-16 23:44:38,081] [INFO] Running command: blastn -query GCA_028063585.1_ASM2806358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35265e95-95d7-4e32-9996-7928e8cb64db/dqc_reference/reference_markers_gtdb.fasta -out GCA_028063585.1_ASM2806358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:44:39,362] [INFO] Task succeeded: Blastn
[2023-06-16 23:44:39,368] [INFO] Selected 25 target genomes.
[2023-06-16 23:44:39,369] [INFO] Target genome list was writen to GCA_028063585.1_ASM2806358v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:44:39,380] [INFO] Task started: fastANI
[2023-06-16 23:44:39,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg132c639f-b6ea-4209-bfab-53977d474642/GCA_028063585.1_ASM2806358v1_genomic.fna.gz --refList GCA_028063585.1_ASM2806358v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028063585.1_ASM2806358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:44:56,621] [INFO] Task succeeded: fastANI
[2023-06-16 23:44:56,645] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 23:44:56,646] [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_003159795.1	s__Bog-793 sp003159795	77.487	169	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Bog-793	95.0	99.80	99.71	0.91	0.89	3	-
GCA_003170375.1	s__Fen-455 sp003170375	76.8202	98	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Fen-455	95.0	98.62	98.35	0.78	0.71	12	-
GCA_003140595.1	s__Fen-455 sp003140595	76.6972	112	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Fen-455	95.0	99.78	99.58	0.92	0.82	27	-
GCA_005888295.1	s__AC-9 sp005888295	76.6087	161	925	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_003164095.1	s__Bog-756 sp003164095	76.5481	186	925	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_003155135.1	s__Bog-515 sp003155135	76.5166	172	925	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_003161255.1	s__Palsa-461 sp003161255	76.5111	137	925	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_003453695.1	s__UBA8190 sp003453695	76.4304	149	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__UBA8190	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805665.1	s__CADCTB01 sp902805665	76.3968	158	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__CADCTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243975.1	s__JAFATL01 sp019243975	76.3758	131	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAFATL01;g__JAFATL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888325.1	s__AC-14 sp005888325	76.3542	178	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__AC-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161575.1	s__PALSA-457 sp003161575	76.3527	106	925	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_003169235.1	s__Bog-473 sp003169235	76.245	151	925	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	-
GCF_009650215.1	s__Actinomarinicola tropica	76.2441	247	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882935.1	s__JADGOP01 sp017882935	76.1866	134	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JADGOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151955.1	s__PALSA-743 sp003151955	76.1434	193	925	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	76.1333	288	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805555.1	s__CADCSY01 sp902805555	76.1328	182	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	76.052	269	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716005.1	s__JADJXE01 sp016716005	75.9935	280	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	75.8588	97	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_016794585.1	s__JAEUJM01 sp016794585	75.849	268	925	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361695.1	s__Curtobacterium flaccumfaciens_B	75.228	143	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308975.1	s__Amycolatopsis sp017308975	75.0444	281	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	75.0179	273	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:44:56,648] [INFO] GTDB search result was written to GCA_028063585.1_ASM2806358v1_genomic.fna/result_gtdb.tsv
[2023-06-16 23:44:56,649] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:44:56,653] [INFO] DFAST_QC result json was written to GCA_028063585.1_ASM2806358v1_genomic.fna/dqc_result.json
[2023-06-16 23:44:56,654] [INFO] DFAST_QC completed!
[2023-06-16 23:44:56,654] [INFO] Total running time: 0h1m17s