[2023-06-18 20:30:04,044] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:30:04,048] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:30:04,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg89eec8d2-0931-4cf0-bc60-fd2248c35d10/dqc_reference
[2023-06-18 20:30:05,304] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:30:05,305] [INFO] Task started: Prodigal
[2023-06-18 20:30:05,305] [INFO] Running command: gunzip -c /var/lib/cwl/stga404004b-5557-484a-870a-f4f61606a827/GCA_018006595.1_ASM1800659v1_genomic.fna.gz | prodigal -d GCA_018006595.1_ASM1800659v1_genomic.fna/cds.fna -a GCA_018006595.1_ASM1800659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:30:10,656] [INFO] Task succeeded: Prodigal
[2023-06-18 20:30:10,656] [INFO] Task started: HMMsearch
[2023-06-18 20:30:10,657] [INFO] Running command: hmmsearch --tblout GCA_018006595.1_ASM1800659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89eec8d2-0931-4cf0-bc60-fd2248c35d10/dqc_reference/reference_markers.hmm GCA_018006595.1_ASM1800659v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:30:10,872] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:30:10,873] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga404004b-5557-484a-870a-f4f61606a827/GCA_018006595.1_ASM1800659v1_genomic.fna.gz]
[2023-06-18 20:30:10,897] [INFO] Query marker FASTA was written to GCA_018006595.1_ASM1800659v1_genomic.fna/markers.fasta
[2023-06-18 20:30:10,897] [INFO] Task started: Blastn
[2023-06-18 20:30:10,897] [INFO] Running command: blastn -query GCA_018006595.1_ASM1800659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89eec8d2-0931-4cf0-bc60-fd2248c35d10/dqc_reference/reference_markers.fasta -out GCA_018006595.1_ASM1800659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:11,508] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:11,514] [INFO] Selected 13 target genomes.
[2023-06-18 20:30:11,515] [INFO] Target genome list was writen to GCA_018006595.1_ASM1800659v1_genomic.fna/target_genomes.txt
[2023-06-18 20:30:11,517] [INFO] Task started: fastANI
[2023-06-18 20:30:11,517] [INFO] Running command: fastANI --query /var/lib/cwl/stga404004b-5557-484a-870a-f4f61606a827/GCA_018006595.1_ASM1800659v1_genomic.fna.gz --refList GCA_018006595.1_ASM1800659v1_genomic.fna/target_genomes.txt --output GCA_018006595.1_ASM1800659v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:30:19,641] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:19,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89eec8d2-0931-4cf0-bc60-fd2248c35d10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:30:19,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89eec8d2-0931-4cf0-bc60-fd2248c35d10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:30:19,655] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:30:19,655] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:30:19,656] [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 limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	79.8495	136	539	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	79.066	140	539	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.9057	133	539	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.8484	134	539	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.3298	135	539	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	78.2739	130	539	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	78.2067	117	539	95	below_threshold
Candidatus Accumulibacter contiguus		GCA_012940005.1	2954381	2954381	type	True	77.3585	104	539	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	77.3231	101	539	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	76.8101	66	539	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	76.7265	58	539	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	76.1337	70	539	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	75.719	58	539	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:30:19,664] [INFO] DFAST Taxonomy check result was written to GCA_018006595.1_ASM1800659v1_genomic.fna/tc_result.tsv
[2023-06-18 20:30:19,665] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:30:19,665] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:30:19,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89eec8d2-0931-4cf0-bc60-fd2248c35d10/dqc_reference/checkm_data
[2023-06-18 20:30:19,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:30:19,695] [INFO] Task started: CheckM
[2023-06-18 20:30:19,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018006595.1_ASM1800659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018006595.1_ASM1800659v1_genomic.fna/checkm_input GCA_018006595.1_ASM1800659v1_genomic.fna/checkm_result
[2023-06-18 20:30:42,854] [INFO] Task succeeded: CheckM
[2023-06-18 20:30:42,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 9.47%
Strain heterogeneity: 23.81%
--------------------------------------------------------------------------------
[2023-06-18 20:30:42,886] [INFO] ===== Completeness check finished =====
[2023-06-18 20:30:42,886] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:30:42,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018006595.1_ASM1800659v1_genomic.fna/markers.fasta)
[2023-06-18 20:30:42,886] [INFO] Task started: Blastn
[2023-06-18 20:30:42,887] [INFO] Running command: blastn -query GCA_018006595.1_ASM1800659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89eec8d2-0931-4cf0-bc60-fd2248c35d10/dqc_reference/reference_markers_gtdb.fasta -out GCA_018006595.1_ASM1800659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:43,751] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:43,755] [INFO] Selected 9 target genomes.
[2023-06-18 20:30:43,755] [INFO] Target genome list was writen to GCA_018006595.1_ASM1800659v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:30:43,756] [INFO] Task started: fastANI
[2023-06-18 20:30:43,756] [INFO] Running command: fastANI --query /var/lib/cwl/stga404004b-5557-484a-870a-f4f61606a827/GCA_018006595.1_ASM1800659v1_genomic.fna.gz --refList GCA_018006595.1_ASM1800659v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018006595.1_ASM1800659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:30:50,039] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:50,053] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 20:30:50,053] [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_017990155.1	s__Propionivibrio sp017990155	90.8131	269	539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.81	98.47	0.75	0.75	3	-
GCA_017995515.1	s__Propionivibrio sp017995515	86.6212	299	539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897745.1	s__66-26 sp001897745	79.7889	172	539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26	95.0	97.97	95.98	0.93	0.89	3	-
GCA_907163075.1	s__Propionivibrio sp907163075	79.5409	193	539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304785.1	s__Propionivibrio sp002304785	79.4096	159	539	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	79.2944	208	539	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	79.1051	141	539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910495.1	s__Propionivibrio sp903910495	78.464	111	539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208425.1	s__JACQYA01 sp016208425	78.1693	125	539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:30:50,055] [INFO] GTDB search result was written to GCA_018006595.1_ASM1800659v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:30:50,056] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:30:50,060] [INFO] DFAST_QC result json was written to GCA_018006595.1_ASM1800659v1_genomic.fna/dqc_result.json
[2023-06-18 20:30:50,061] [INFO] DFAST_QC completed!
[2023-06-18 20:30:50,061] [INFO] Total running time: 0h0m46s