[2023-06-19 14:28:51,518] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:28:51,521] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:28:51,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg246219f7-ea2a-46e9-bc14-ab32d4eb7d50/dqc_reference
[2023-06-19 14:28:53,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:28:53,578] [INFO] Task started: Prodigal
[2023-06-19 14:28:53,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg66857f4a-802c-4cc5-98c3-2a0b745156e4/GCA_018262175.1_ASM1826217v1_genomic.fna.gz | prodigal -d GCA_018262175.1_ASM1826217v1_genomic.fna/cds.fna -a GCA_018262175.1_ASM1826217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:01,345] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:01,345] [INFO] Task started: HMMsearch
[2023-06-19 14:29:01,346] [INFO] Running command: hmmsearch --tblout GCA_018262175.1_ASM1826217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg246219f7-ea2a-46e9-bc14-ab32d4eb7d50/dqc_reference/reference_markers.hmm GCA_018262175.1_ASM1826217v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:01,565] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:01,569] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg66857f4a-802c-4cc5-98c3-2a0b745156e4/GCA_018262175.1_ASM1826217v1_genomic.fna.gz]
[2023-06-19 14:29:01,606] [INFO] Query marker FASTA was written to GCA_018262175.1_ASM1826217v1_genomic.fna/markers.fasta
[2023-06-19 14:29:01,607] [INFO] Task started: Blastn
[2023-06-19 14:29:01,607] [INFO] Running command: blastn -query GCA_018262175.1_ASM1826217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg246219f7-ea2a-46e9-bc14-ab32d4eb7d50/dqc_reference/reference_markers.fasta -out GCA_018262175.1_ASM1826217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:02,293] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:02,298] [INFO] Selected 25 target genomes.
[2023-06-19 14:29:02,298] [INFO] Target genome list was writen to GCA_018262175.1_ASM1826217v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:02,305] [INFO] Task started: fastANI
[2023-06-19 14:29:02,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg66857f4a-802c-4cc5-98c3-2a0b745156e4/GCA_018262175.1_ASM1826217v1_genomic.fna.gz --refList GCA_018262175.1_ASM1826217v1_genomic.fna/target_genomes.txt --output GCA_018262175.1_ASM1826217v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:29:18,199] [INFO] Task succeeded: fastANI
[2023-06-19 14:29:18,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg246219f7-ea2a-46e9-bc14-ab32d4eb7d50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:29:18,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg246219f7-ea2a-46e9-bc14-ab32d4eb7d50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:29:18,224] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:29:18,224] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:29:18,224] [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
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	79.2721	137	693	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	78.9642	126	693	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.8326	88	693	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.782	90	693	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.7412	117	693	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.7166	73	693	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.6217	104	693	95	below_threshold
Usitatibacter palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	76.5984	60	693	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	76.5011	94	693	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	76.4272	88	693	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	76.42	87	693	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.4156	96	693	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	76.4062	104	693	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.2865	133	693	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2247	62	693	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.1872	64	693	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	76.0882	95	693	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	76.0418	83	693	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	76.0205	82	693	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	75.9766	121	693	95	below_threshold
Paraburkholderia youngii	strain=JPY169	GCA_013366925.1	2782701	2782701	type	True	75.7346	90	693	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	75.7165	111	693	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	75.7097	110	693	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	75.6971	98	693	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.665	55	693	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:29:18,228] [INFO] DFAST Taxonomy check result was written to GCA_018262175.1_ASM1826217v1_genomic.fna/tc_result.tsv
[2023-06-19 14:29:18,229] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:29:18,229] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:29:18,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg246219f7-ea2a-46e9-bc14-ab32d4eb7d50/dqc_reference/checkm_data
[2023-06-19 14:29:18,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:29:18,265] [INFO] Task started: CheckM
[2023-06-19 14:29:18,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018262175.1_ASM1826217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018262175.1_ASM1826217v1_genomic.fna/checkm_input GCA_018262175.1_ASM1826217v1_genomic.fna/checkm_result
[2023-06-19 14:29:45,927] [INFO] Task succeeded: CheckM
[2023-06-19 14:29:45,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.79%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:29:45,959] [INFO] ===== Completeness check finished =====
[2023-06-19 14:29:45,959] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:29:45,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018262175.1_ASM1826217v1_genomic.fna/markers.fasta)
[2023-06-19 14:29:45,960] [INFO] Task started: Blastn
[2023-06-19 14:29:45,960] [INFO] Running command: blastn -query GCA_018262175.1_ASM1826217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg246219f7-ea2a-46e9-bc14-ab32d4eb7d50/dqc_reference/reference_markers_gtdb.fasta -out GCA_018262175.1_ASM1826217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:46,945] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:46,950] [INFO] Selected 17 target genomes.
[2023-06-19 14:29:46,950] [INFO] Target genome list was writen to GCA_018262175.1_ASM1826217v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:29:46,986] [INFO] Task started: fastANI
[2023-06-19 14:29:46,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg66857f4a-802c-4cc5-98c3-2a0b745156e4/GCA_018262175.1_ASM1826217v1_genomic.fna.gz --refList GCA_018262175.1_ASM1826217v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018262175.1_ASM1826217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:29:56,174] [INFO] Task succeeded: fastANI
[2023-06-19 14:29:56,189] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:29:56,189] [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_003820645.1	s__Ga0077527 sp003820645	97.5963	483	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__Ga0077527	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903933915.1	s__Ga0077527 sp903933915	80.6142	383	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__Ga0077527	95.0	99.39	99.32	0.93	0.92	3	-
GCA_001464815.1	s__Ga0077527 sp001464815	80.049	349	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__Ga0077527	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	78.9321	156	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016177355.1	s__SG8-41 sp016177355	77.4559	108	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192825.1	s__SG8-41 sp016192825	77.2277	176	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330925.1	s__SG8-41 sp011330925	77.2095	86	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001772005.1	s__DSOT01 sp001772005	77.1825	181	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__DSOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825845.1	s__UBA5216 sp902825845	77.1605	168	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002412495.1	s__UBA5216 sp002412495	76.597	147	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	99.91	99.91	0.93	0.93	2	-
GCF_003634965.1	s__Azonexus fungiphilus	76.5011	94	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.36	98.36	0.85	0.85	2	-
GCF_016653115.1	s__Rhodocyclus purpureus	76.3949	97	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214175.1	s__JACRPB01 sp016214175	75.9199	92	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRPB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:29:56,192] [INFO] GTDB search result was written to GCA_018262175.1_ASM1826217v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:29:56,193] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:29:56,197] [INFO] DFAST_QC result json was written to GCA_018262175.1_ASM1826217v1_genomic.fna/dqc_result.json
[2023-06-19 14:29:56,198] [INFO] DFAST_QC completed!
[2023-06-19 14:29:56,198] [INFO] Total running time: 0h1m5s