[2023-06-19 00:04:56,498] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:04:56,500] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:04:56,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg35309d98-13e9-411b-8b7d-92660eacb41d/dqc_reference
[2023-06-19 00:05:00,055] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:05:00,056] [INFO] Task started: Prodigal
[2023-06-19 00:05:00,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fab2438-96e5-4870-b722-2c35678d6f3c/GCA_018607025.1_ASM1860702v1_genomic.fna.gz | prodigal -d GCA_018607025.1_ASM1860702v1_genomic.fna/cds.fna -a GCA_018607025.1_ASM1860702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:05:02,039] [INFO] Task succeeded: Prodigal
[2023-06-19 00:05:02,039] [INFO] Task started: HMMsearch
[2023-06-19 00:05:02,039] [INFO] Running command: hmmsearch --tblout GCA_018607025.1_ASM1860702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35309d98-13e9-411b-8b7d-92660eacb41d/dqc_reference/reference_markers.hmm GCA_018607025.1_ASM1860702v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:05:02,247] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:05:02,251] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6fab2438-96e5-4870-b722-2c35678d6f3c/GCA_018607025.1_ASM1860702v1_genomic.fna.gz]
[2023-06-19 00:05:02,295] [INFO] Query marker FASTA was written to GCA_018607025.1_ASM1860702v1_genomic.fna/markers.fasta
[2023-06-19 00:05:02,296] [INFO] Task started: Blastn
[2023-06-19 00:05:02,296] [INFO] Running command: blastn -query GCA_018607025.1_ASM1860702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35309d98-13e9-411b-8b7d-92660eacb41d/dqc_reference/reference_markers.fasta -out GCA_018607025.1_ASM1860702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:05,553] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:05,580] [INFO] Selected 13 target genomes.
[2023-06-19 00:05:05,580] [INFO] Target genome list was writen to GCA_018607025.1_ASM1860702v1_genomic.fna/target_genomes.txt
[2023-06-19 00:05:05,582] [INFO] Task started: fastANI
[2023-06-19 00:05:05,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fab2438-96e5-4870-b722-2c35678d6f3c/GCA_018607025.1_ASM1860702v1_genomic.fna.gz --refList GCA_018607025.1_ASM1860702v1_genomic.fna/target_genomes.txt --output GCA_018607025.1_ASM1860702v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:05:12,650] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:12,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35309d98-13e9-411b-8b7d-92660eacb41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:05:12,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35309d98-13e9-411b-8b7d-92660eacb41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:05:12,662] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:05:12,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:05:12,663] [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
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	83.2059	136	180	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	82.5729	135	180	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	82.0748	142	180	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	81.9927	135	180	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	81.9881	140	180	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	81.9415	134	180	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	81.8953	139	180	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	81.6516	123	180	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.5994	109	180	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.4691	78	180	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.281	87	180	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.1376	83	180	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	77.5592	66	180	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:05:12,670] [INFO] DFAST Taxonomy check result was written to GCA_018607025.1_ASM1860702v1_genomic.fna/tc_result.tsv
[2023-06-19 00:05:12,671] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:05:12,671] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:05:12,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35309d98-13e9-411b-8b7d-92660eacb41d/dqc_reference/checkm_data
[2023-06-19 00:05:12,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:05:12,700] [INFO] Task started: CheckM
[2023-06-19 00:05:12,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607025.1_ASM1860702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607025.1_ASM1860702v1_genomic.fna/checkm_input GCA_018607025.1_ASM1860702v1_genomic.fna/checkm_result
[2023-06-19 00:05:26,022] [INFO] Task succeeded: CheckM
[2023-06-19 00:05:26,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:05:26,052] [INFO] ===== Completeness check finished =====
[2023-06-19 00:05:26,052] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:05:26,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607025.1_ASM1860702v1_genomic.fna/markers.fasta)
[2023-06-19 00:05:26,053] [INFO] Task started: Blastn
[2023-06-19 00:05:26,053] [INFO] Running command: blastn -query GCA_018607025.1_ASM1860702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35309d98-13e9-411b-8b7d-92660eacb41d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607025.1_ASM1860702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:26,933] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:26,938] [INFO] Selected 8 target genomes.
[2023-06-19 00:05:26,938] [INFO] Target genome list was writen to GCA_018607025.1_ASM1860702v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:05:26,940] [INFO] Task started: fastANI
[2023-06-19 00:05:26,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fab2438-96e5-4870-b722-2c35678d6f3c/GCA_018607025.1_ASM1860702v1_genomic.fna.gz --refList GCA_018607025.1_ASM1860702v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607025.1_ASM1860702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:05:30,609] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:30,624] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 00:05:30,624] [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
GCF_007556755.1	s__Tepidimonas fonticaldi	83.2049	136	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCF_007556705.1	s__Tepidimonas thermarum	82.6328	134	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556605.1	s__Tepidimonas sediminis	82.0748	142	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556675.1	s__Tepidimonas taiwanensis	81.9673	141	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	-
GCF_004342625.1	s__Tepidimonas ignava	81.9614	135	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007556585.1	s__Tepidimonas aquatica	81.9187	130	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556595.1	s__Tepidimonas alkaliphilus	81.5758	125	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363315.1	s__Tepidicella xavieri	79.4522	107	180	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:05:30,626] [INFO] GTDB search result was written to GCA_018607025.1_ASM1860702v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:05:30,627] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:05:30,639] [INFO] DFAST_QC result json was written to GCA_018607025.1_ASM1860702v1_genomic.fna/dqc_result.json
[2023-06-19 00:05:30,639] [INFO] DFAST_QC completed!
[2023-06-19 00:05:30,640] [INFO] Total running time: 0h0m34s