[2023-06-08 03:14:36,124] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:36,126] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:36,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ed40de9-4451-4df0-a820-d298163fb7ef/dqc_reference
[2023-06-08 03:14:39,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:39,370] [INFO] Task started: Prodigal
[2023-06-08 03:14:39,371] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e68eaef-d927-49f3-b4cf-2c63b8b746fc/GCA_945899335.1_ZH-13nov19-181_genomic.fna.gz | prodigal -d GCA_945899335.1_ZH-13nov19-181_genomic.fna/cds.fna -a GCA_945899335.1_ZH-13nov19-181_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:44,307] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:44,308] [INFO] Task started: HMMsearch
[2023-06-08 03:14:44,308] [INFO] Running command: hmmsearch --tblout GCA_945899335.1_ZH-13nov19-181_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ed40de9-4451-4df0-a820-d298163fb7ef/dqc_reference/reference_markers.hmm GCA_945899335.1_ZH-13nov19-181_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:44,497] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:44,499] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg5e68eaef-d927-49f3-b4cf-2c63b8b746fc/GCA_945899335.1_ZH-13nov19-181_genomic.fna.gz]
[2023-06-08 03:14:44,522] [INFO] Query marker FASTA was written to GCA_945899335.1_ZH-13nov19-181_genomic.fna/markers.fasta
[2023-06-08 03:14:44,523] [INFO] Task started: Blastn
[2023-06-08 03:14:44,523] [INFO] Running command: blastn -query GCA_945899335.1_ZH-13nov19-181_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed40de9-4451-4df0-a820-d298163fb7ef/dqc_reference/reference_markers.fasta -out GCA_945899335.1_ZH-13nov19-181_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:45,058] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:45,062] [INFO] Selected 10 target genomes.
[2023-06-08 03:14:45,062] [INFO] Target genome list was writen to GCA_945899335.1_ZH-13nov19-181_genomic.fna/target_genomes.txt
[2023-06-08 03:14:45,063] [INFO] Task started: fastANI
[2023-06-08 03:14:45,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e68eaef-d927-49f3-b4cf-2c63b8b746fc/GCA_945899335.1_ZH-13nov19-181_genomic.fna.gz --refList GCA_945899335.1_ZH-13nov19-181_genomic.fna/target_genomes.txt --output GCA_945899335.1_ZH-13nov19-181_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:52,239] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:52,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ed40de9-4451-4df0-a820-d298163fb7ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:52,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ed40de9-4451-4df0-a820-d298163fb7ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:52,252] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:14:52,253] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:14:52,253] [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
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.6534	84	415	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.6416	123	415	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.5157	108	415	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	77.0736	59	415	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.6617	65	415	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.6433	72	415	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	76.6297	55	415	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.1902	50	415	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:14:52,255] [INFO] DFAST Taxonomy check result was written to GCA_945899335.1_ZH-13nov19-181_genomic.fna/tc_result.tsv
[2023-06-08 03:14:52,256] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:52,256] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:52,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ed40de9-4451-4df0-a820-d298163fb7ef/dqc_reference/checkm_data
[2023-06-08 03:14:52,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:52,275] [INFO] Task started: CheckM
[2023-06-08 03:14:52,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945899335.1_ZH-13nov19-181_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945899335.1_ZH-13nov19-181_genomic.fna/checkm_input GCA_945899335.1_ZH-13nov19-181_genomic.fna/checkm_result
[2023-06-08 03:15:13,622] [INFO] Task succeeded: CheckM
[2023-06-08 03:15:13,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 03:15:13,658] [INFO] ===== Completeness check finished =====
[2023-06-08 03:15:13,659] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:15:13,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945899335.1_ZH-13nov19-181_genomic.fna/markers.fasta)
[2023-06-08 03:15:13,660] [INFO] Task started: Blastn
[2023-06-08 03:15:13,660] [INFO] Running command: blastn -query GCA_945899335.1_ZH-13nov19-181_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed40de9-4451-4df0-a820-d298163fb7ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_945899335.1_ZH-13nov19-181_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:15:14,283] [INFO] Task succeeded: Blastn
[2023-06-08 03:15:14,288] [INFO] Selected 8 target genomes.
[2023-06-08 03:15:14,288] [INFO] Target genome list was writen to GCA_945899335.1_ZH-13nov19-181_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:15:14,292] [INFO] Task started: fastANI
[2023-06-08 03:15:14,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e68eaef-d927-49f3-b4cf-2c63b8b746fc/GCA_945899335.1_ZH-13nov19-181_genomic.fna.gz --refList GCA_945899335.1_ZH-13nov19-181_genomic.fna/target_genomes_gtdb.txt --output GCA_945899335.1_ZH-13nov19-181_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:15:17,555] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:17,564] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 03:15:17,564] [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_013205525.1	s__Limnohabitans sp013205525	82.3073	224	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903956845.1	s__Limnohabitans sp903956845	79.754	212	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009921465.1	s__Limnohabitans sp009921465	78.5297	68	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009925585.1	s__Limnohabitans sp009925585	78.1028	190	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.01	99.01	0.84	0.84	2	-
GCA_005789825.1	s__Limnohabitans sp005789825	77.984	155	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	96.68	96.68	0.84	0.84	2	-
GCA_009927195.1	s__Limnohabitans sp009927195	77.6129	76	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269345.1	s__Limnohabitans_A sp001269345	77.5194	98	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916355.1	s__Limnohabitans_A sp903916355	77.4726	108	415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.87	99.87	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-08 03:15:17,566] [INFO] GTDB search result was written to GCA_945899335.1_ZH-13nov19-181_genomic.fna/result_gtdb.tsv
[2023-06-08 03:15:17,567] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:15:17,570] [INFO] DFAST_QC result json was written to GCA_945899335.1_ZH-13nov19-181_genomic.fna/dqc_result.json
[2023-06-08 03:15:17,570] [INFO] DFAST_QC completed!
[2023-06-08 03:15:17,571] [INFO] Total running time: 0h0m41s