[2023-06-28 12:14:23,571] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:14:23,583] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:14:23,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a289eeb-d0da-42c5-942d-7d8ef565914e/dqc_reference
[2023-06-28 12:14:24,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:14:24,962] [INFO] Task started: Prodigal
[2023-06-28 12:14:24,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg95779cfc-8e9d-4886-a722-ce0f0b6087e1/GCA_020049495.1_ASM2004949v1_genomic.fna.gz | prodigal -d GCA_020049495.1_ASM2004949v1_genomic.fna/cds.fna -a GCA_020049495.1_ASM2004949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:14:34,798] [INFO] Task succeeded: Prodigal
[2023-06-28 12:14:34,798] [INFO] Task started: HMMsearch
[2023-06-28 12:14:34,799] [INFO] Running command: hmmsearch --tblout GCA_020049495.1_ASM2004949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a289eeb-d0da-42c5-942d-7d8ef565914e/dqc_reference/reference_markers.hmm GCA_020049495.1_ASM2004949v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:14:35,085] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:14:35,086] [INFO] Found 6/6 markers.
[2023-06-28 12:14:35,132] [INFO] Query marker FASTA was written to GCA_020049495.1_ASM2004949v1_genomic.fna/markers.fasta
[2023-06-28 12:14:35,133] [INFO] Task started: Blastn
[2023-06-28 12:14:35,133] [INFO] Running command: blastn -query GCA_020049495.1_ASM2004949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a289eeb-d0da-42c5-942d-7d8ef565914e/dqc_reference/reference_markers.fasta -out GCA_020049495.1_ASM2004949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:14:36,039] [INFO] Task succeeded: Blastn
[2023-06-28 12:14:36,044] [INFO] Selected 18 target genomes.
[2023-06-28 12:14:36,044] [INFO] Target genome list was writen to GCA_020049495.1_ASM2004949v1_genomic.fna/target_genomes.txt
[2023-06-28 12:14:36,052] [INFO] Task started: fastANI
[2023-06-28 12:14:36,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg95779cfc-8e9d-4886-a722-ce0f0b6087e1/GCA_020049495.1_ASM2004949v1_genomic.fna.gz --refList GCA_020049495.1_ASM2004949v1_genomic.fna/target_genomes.txt --output GCA_020049495.1_ASM2004949v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:14:49,233] [INFO] Task succeeded: fastANI
[2023-06-28 12:14:49,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a289eeb-d0da-42c5-942d-7d8ef565914e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:14:49,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a289eeb-d0da-42c5-942d-7d8ef565914e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:14:49,249] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:14:49,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:14:49,249] [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
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	78.5252	348	1063	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	78.4826	266	1063	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.2391	269	1063	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.2281	273	1063	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.1822	221	1063	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.8379	218	1063	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.8316	204	1063	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.7315	226	1063	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.5882	168	1063	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.522	169	1063	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	77.2942	228	1063	95	below_threshold
Candidatus Accumulibacter contiguus		GCA_012940005.1	2954381	2954381	type	True	77.2684	229	1063	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.7715	103	1063	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.7307	103	1063	95	below_threshold
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	76.6793	95	1063	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	76.4953	98	1063	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	76.3396	71	1063	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	76.1401	78	1063	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:14:49,251] [INFO] DFAST Taxonomy check result was written to GCA_020049495.1_ASM2004949v1_genomic.fna/tc_result.tsv
[2023-06-28 12:14:49,257] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:14:49,257] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:14:49,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a289eeb-d0da-42c5-942d-7d8ef565914e/dqc_reference/checkm_data
[2023-06-28 12:14:49,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:14:49,303] [INFO] Task started: CheckM
[2023-06-28 12:14:49,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020049495.1_ASM2004949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020049495.1_ASM2004949v1_genomic.fna/checkm_input GCA_020049495.1_ASM2004949v1_genomic.fna/checkm_result
[2023-06-28 12:15:22,521] [INFO] Task succeeded: CheckM
[2023-06-28 12:15:22,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:15:22,544] [INFO] ===== Completeness check finished =====
[2023-06-28 12:15:22,544] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:15:22,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020049495.1_ASM2004949v1_genomic.fna/markers.fasta)
[2023-06-28 12:15:22,545] [INFO] Task started: Blastn
[2023-06-28 12:15:22,545] [INFO] Running command: blastn -query GCA_020049495.1_ASM2004949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a289eeb-d0da-42c5-942d-7d8ef565914e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020049495.1_ASM2004949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:15:24,153] [INFO] Task succeeded: Blastn
[2023-06-28 12:15:24,158] [INFO] Selected 12 target genomes.
[2023-06-28 12:15:24,159] [INFO] Target genome list was writen to GCA_020049495.1_ASM2004949v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:15:24,166] [INFO] Task started: fastANI
[2023-06-28 12:15:24,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg95779cfc-8e9d-4886-a722-ce0f0b6087e1/GCA_020049495.1_ASM2004949v1_genomic.fna.gz --refList GCA_020049495.1_ASM2004949v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020049495.1_ASM2004949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:15:32,883] [INFO] Task succeeded: fastANI
[2023-06-28 12:15:32,903] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:15:32,903] [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_903910495.1	s__Propionivibrio sp903910495	90.2251	610	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709335.1	s__Propionivibrio sp016709335	80.4981	479	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.69	98.69	0.87	0.87	2	-
GCA_016790145.1	s__Propionivibrio sp016790145	80.4334	427	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_907163075.1	s__Propionivibrio sp907163075	80.1668	485	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886975.1	s__Propionivibrio sp903886975	79.8285	472	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262095.1	s__Propionivibrio sp018262095	79.7363	496	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089945.1	s__Propionivibrio aalborgensis	79.0619	300	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.22	98.12	0.81	0.78	4	-
GCA_017990155.1	s__Propionivibrio sp017990155	78.839	241	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.81	98.47	0.75	0.75	3	-
GCA_016705685.1	s__Propionivibrio sp016705685	78.7802	327	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	99.41	99.26	0.91	0.89	5	-
GCA_016208425.1	s__JACQYA01 sp016208425	78.5373	269	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099695.1	s__Propionivibrio dicarboxylicus	78.5245	348	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653115.1	s__Rhodocyclus purpureus	78.1657	222	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:15:32,906] [INFO] GTDB search result was written to GCA_020049495.1_ASM2004949v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:15:32,907] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:15:32,914] [INFO] DFAST_QC result json was written to GCA_020049495.1_ASM2004949v1_genomic.fna/dqc_result.json
[2023-06-28 12:15:32,914] [INFO] DFAST_QC completed!
[2023-06-28 12:15:32,914] [INFO] Total running time: 0h1m9s