[2023-06-28 00:32:34,470] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:32:34,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:32:34,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc1e2002-ef93-47d9-97f8-7e8e5871edfe/dqc_reference
[2023-06-28 00:32:35,651] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:32:35,651] [INFO] Task started: Prodigal
[2023-06-28 00:32:35,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f7002e2-8aae-4346-98f2-4d7808c06b4d/GCA_027315405.1_ASM2731540v1_genomic.fna.gz | prodigal -d GCA_027315405.1_ASM2731540v1_genomic.fna/cds.fna -a GCA_027315405.1_ASM2731540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:32:44,233] [INFO] Task succeeded: Prodigal
[2023-06-28 00:32:44,234] [INFO] Task started: HMMsearch
[2023-06-28 00:32:44,234] [INFO] Running command: hmmsearch --tblout GCA_027315405.1_ASM2731540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc1e2002-ef93-47d9-97f8-7e8e5871edfe/dqc_reference/reference_markers.hmm GCA_027315405.1_ASM2731540v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:32:44,418] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:32:44,419] [INFO] Found 6/6 markers.
[2023-06-28 00:32:44,447] [INFO] Query marker FASTA was written to GCA_027315405.1_ASM2731540v1_genomic.fna/markers.fasta
[2023-06-28 00:32:44,447] [INFO] Task started: Blastn
[2023-06-28 00:32:44,447] [INFO] Running command: blastn -query GCA_027315405.1_ASM2731540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc1e2002-ef93-47d9-97f8-7e8e5871edfe/dqc_reference/reference_markers.fasta -out GCA_027315405.1_ASM2731540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:32:45,193] [INFO] Task succeeded: Blastn
[2023-06-28 00:32:45,196] [INFO] Selected 32 target genomes.
[2023-06-28 00:32:45,197] [INFO] Target genome list was writen to GCA_027315405.1_ASM2731540v1_genomic.fna/target_genomes.txt
[2023-06-28 00:32:45,197] [INFO] Task started: fastANI
[2023-06-28 00:32:45,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7002e2-8aae-4346-98f2-4d7808c06b4d/GCA_027315405.1_ASM2731540v1_genomic.fna.gz --refList GCA_027315405.1_ASM2731540v1_genomic.fna/target_genomes.txt --output GCA_027315405.1_ASM2731540v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:33:03,679] [INFO] Task succeeded: fastANI
[2023-06-28 00:33:03,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc1e2002-ef93-47d9-97f8-7e8e5871edfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:33:03,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc1e2002-ef93-47d9-97f8-7e8e5871edfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:33:03,690] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:33:03,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:33:03,690] [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
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.6888	59	899	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.6333	76	899	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.3617	56	899	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2813	68	899	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.1814	73	899	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	76.1726	68	899	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.1711	78	899	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	75.9888	56	899	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	75.916	58	899	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	75.7371	51	899	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.6962	66	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:33:03,694] [INFO] DFAST Taxonomy check result was written to GCA_027315405.1_ASM2731540v1_genomic.fna/tc_result.tsv
[2023-06-28 00:33:03,695] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:33:03,695] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:33:03,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc1e2002-ef93-47d9-97f8-7e8e5871edfe/dqc_reference/checkm_data
[2023-06-28 00:33:03,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:33:03,726] [INFO] Task started: CheckM
[2023-06-28 00:33:03,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027315405.1_ASM2731540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027315405.1_ASM2731540v1_genomic.fna/checkm_input GCA_027315405.1_ASM2731540v1_genomic.fna/checkm_result
[2023-06-28 00:33:32,097] [INFO] Task succeeded: CheckM
[2023-06-28 00:33:32,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:33:32,116] [INFO] ===== Completeness check finished =====
[2023-06-28 00:33:32,116] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:33:32,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027315405.1_ASM2731540v1_genomic.fna/markers.fasta)
[2023-06-28 00:33:32,116] [INFO] Task started: Blastn
[2023-06-28 00:33:32,116] [INFO] Running command: blastn -query GCA_027315405.1_ASM2731540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc1e2002-ef93-47d9-97f8-7e8e5871edfe/dqc_reference/reference_markers_gtdb.fasta -out GCA_027315405.1_ASM2731540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:33:33,425] [INFO] Task succeeded: Blastn
[2023-06-28 00:33:33,428] [INFO] Selected 32 target genomes.
[2023-06-28 00:33:33,428] [INFO] Target genome list was writen to GCA_027315405.1_ASM2731540v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:33:33,430] [INFO] Task started: fastANI
[2023-06-28 00:33:33,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7002e2-8aae-4346-98f2-4d7808c06b4d/GCA_027315405.1_ASM2731540v1_genomic.fna.gz --refList GCA_027315405.1_ASM2731540v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027315405.1_ASM2731540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:33:56,560] [INFO] Task succeeded: fastANI
[2023-06-28 00:33:56,571] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:33:56,571] [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_018971605.1	s__REEB76 sp018971605	78.0822	232	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__REEB76;f__REEB76;g__REEB76	95.0	99.78	99.78	0.93	0.93	2	-
GCA_015494295.1	s__Thiogranum sp015494295	76.7059	62	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	76.6888	59	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	76.6333	76	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	76.3617	56	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967035.1	s__Aerosticca soli	76.3331	57	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Aerosticca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.3012	52	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348725.1	s__GCA-013348725 sp013348725	76.2055	56	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	76.1936	77	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012275375.1	s__Dyella sp012275375	76.0282	78	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_012939995.1	s__Competibacter phosphatis	75.9765	55	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	75.7898	64	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012769535.1	s__Methylococcus sp012769535	75.7371	51	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:33:56,573] [INFO] GTDB search result was written to GCA_027315405.1_ASM2731540v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:33:56,573] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:33:56,577] [INFO] DFAST_QC result json was written to GCA_027315405.1_ASM2731540v1_genomic.fna/dqc_result.json
[2023-06-28 00:33:56,577] [INFO] DFAST_QC completed!
[2023-06-28 00:33:56,577] [INFO] Total running time: 0h1m22s