[2023-06-30 23:06:48,215] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:06:48,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:06:48,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg298b84e1-f4fb-4e40-8f4b-96133ba72905/dqc_reference
[2023-06-30 23:06:49,448] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:06:49,449] [INFO] Task started: Prodigal
[2023-06-30 23:06:49,449] [INFO] Running command: gunzip -c /var/lib/cwl/stg97c19fb2-e080-4548-8017-620aab694c56/GCA_016708795.1_ASM1670879v1_genomic.fna.gz | prodigal -d GCA_016708795.1_ASM1670879v1_genomic.fna/cds.fna -a GCA_016708795.1_ASM1670879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:07:03,199] [INFO] Task succeeded: Prodigal
[2023-06-30 23:07:03,200] [INFO] Task started: HMMsearch
[2023-06-30 23:07:03,200] [INFO] Running command: hmmsearch --tblout GCA_016708795.1_ASM1670879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg298b84e1-f4fb-4e40-8f4b-96133ba72905/dqc_reference/reference_markers.hmm GCA_016708795.1_ASM1670879v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:07:03,497] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:07:03,498] [INFO] Found 6/6 markers.
[2023-06-30 23:07:03,545] [INFO] Query marker FASTA was written to GCA_016708795.1_ASM1670879v1_genomic.fna/markers.fasta
[2023-06-30 23:07:03,546] [INFO] Task started: Blastn
[2023-06-30 23:07:03,546] [INFO] Running command: blastn -query GCA_016708795.1_ASM1670879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298b84e1-f4fb-4e40-8f4b-96133ba72905/dqc_reference/reference_markers.fasta -out GCA_016708795.1_ASM1670879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:07:04,353] [INFO] Task succeeded: Blastn
[2023-06-30 23:07:04,357] [INFO] Selected 30 target genomes.
[2023-06-30 23:07:04,357] [INFO] Target genome list was writen to GCA_016708795.1_ASM1670879v1_genomic.fna/target_genomes.txt
[2023-06-30 23:07:04,361] [INFO] Task started: fastANI
[2023-06-30 23:07:04,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c19fb2-e080-4548-8017-620aab694c56/GCA_016708795.1_ASM1670879v1_genomic.fna.gz --refList GCA_016708795.1_ASM1670879v1_genomic.fna/target_genomes.txt --output GCA_016708795.1_ASM1670879v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:07:28,113] [INFO] Task succeeded: fastANI
[2023-06-30 23:07:28,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg298b84e1-f4fb-4e40-8f4b-96133ba72905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:07:28,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg298b84e1-f4fb-4e40-8f4b-96133ba72905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:07:28,135] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:07:28,135] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 23:07:28,135] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.9483	249	1440	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.6842	263	1440	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.4594	158	1440	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.3344	186	1440	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.1293	172	1440	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	75.6516	66	1440	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	75.6006	98	1440	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	75.5454	121	1440	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	75.5245	119	1440	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	75.4658	148	1440	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	75.39	186	1440	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	75.362	146	1440	95	below_threshold
Actinomyces howellii	strain=NCTC11636	GCA_900637165.1	52771	52771	type	True	75.321	76	1440	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	75.3203	180	1440	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_023383595.1	477641	477641	type	True	75.3186	176	1440	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	75.3157	114	1440	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	75.3071	154	1440	95	below_threshold
Longispora fulva	strain=DSM 45356	GCA_015751905.1	619741	619741	type	True	75.2962	163	1440	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	75.2915	141	1440	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	75.2593	214	1440	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	75.2426	181	1440	95	below_threshold
Longispora fulva	strain=NBRC 105670	GCA_016862835.1	619741	619741	type	True	75.2252	159	1440	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	75.2111	76	1440	95	below_threshold
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	75.2069	204	1440	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	75.2014	161	1440	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	75.1798	218	1440	95	below_threshold
Actinocatenispora comari	strain=NUM-2625	GCA_017312725.1	2807577	2807577	type	True	75.0569	198	1440	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	74.8844	79	1440	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 23:07:28,137] [INFO] DFAST Taxonomy check result was written to GCA_016708795.1_ASM1670879v1_genomic.fna/tc_result.tsv
[2023-06-30 23:07:28,138] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:07:28,138] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:07:28,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg298b84e1-f4fb-4e40-8f4b-96133ba72905/dqc_reference/checkm_data
[2023-06-30 23:07:28,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:07:28,187] [INFO] Task started: CheckM
[2023-06-30 23:07:28,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708795.1_ASM1670879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708795.1_ASM1670879v1_genomic.fna/checkm_input GCA_016708795.1_ASM1670879v1_genomic.fna/checkm_result
[2023-06-30 23:08:16,820] [INFO] Task succeeded: CheckM
[2023-06-30 23:08:16,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:08:16,845] [INFO] ===== Completeness check finished =====
[2023-06-30 23:08:16,845] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:08:16,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708795.1_ASM1670879v1_genomic.fna/markers.fasta)
[2023-06-30 23:08:16,846] [INFO] Task started: Blastn
[2023-06-30 23:08:16,846] [INFO] Running command: blastn -query GCA_016708795.1_ASM1670879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298b84e1-f4fb-4e40-8f4b-96133ba72905/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708795.1_ASM1670879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:08:18,070] [INFO] Task succeeded: Blastn
[2023-06-30 23:08:18,076] [INFO] Selected 21 target genomes.
[2023-06-30 23:08:18,076] [INFO] Target genome list was writen to GCA_016708795.1_ASM1670879v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:08:18,082] [INFO] Task started: fastANI
[2023-06-30 23:08:18,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c19fb2-e080-4548-8017-620aab694c56/GCA_016708795.1_ASM1670879v1_genomic.fna.gz --refList GCA_016708795.1_ASM1670879v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708795.1_ASM1670879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:08:31,538] [INFO] Task succeeded: fastANI
[2023-06-30 23:08:31,557] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:08:31,558] [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_016719385.1	s__Microthrix sp002473265	99.0462	1271	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	98.81	98.46	0.90	0.86	7	conclusive
GCF_000299415.1	s__Microthrix parvicella	81.9723	808	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	99.08	98.57	0.94	0.83	22	-
GCF_009650215.1	s__Actinomarinicola tropica	76.9474	250	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	76.83	168	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_016649895.1	s__Actinomarinicola sp016649895	76.8226	192	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.7747	230	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_007121465.1	s__SKKL01 sp007121465	76.7007	173	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	76.6723	218	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118345.1	s__SKRR01 sp007118345	76.5514	196	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SKRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699605.1	s__WLNW01 sp009699605	76.3159	116	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__WLNW01;g__WLNW01	95.0	99.58	99.52	0.88	0.87	4	-
GCA_005777415.1	s__SXMI01 sp005777415	76.199	110	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.41	99.40	0.88	0.87	3	-
GCA_003697065.1	s__J010 sp003697065	76.1787	147	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925745.1	s__SXMI01 sp903925745	76.1649	177	1440	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882995.1	s__Chersky-840 sp017882995	75.4833	85	1440	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_018335555.1	s__Egicoccus sp018335555	75.4818	92	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007673235.1	s__Curtobacterium pusillum_C	75.3892	73	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637165.1	s__Actinomyces howellii	75.3007	78	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003336425.1	s__Marinitenerispora sediminis	75.2498	131	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_000379645.1	s__Actinoplanes globisporus	75.2081	203	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:08:31,560] [INFO] GTDB search result was written to GCA_016708795.1_ASM1670879v1_genomic.fna/result_gtdb.tsv
[2023-06-30 23:08:31,561] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:08:31,566] [INFO] DFAST_QC result json was written to GCA_016708795.1_ASM1670879v1_genomic.fna/dqc_result.json
[2023-06-30 23:08:31,566] [INFO] DFAST_QC completed!
[2023-06-30 23:08:31,566] [INFO] Total running time: 0h1m43s