[2023-06-29 20:05:53,218] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:05:53,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:05:53,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1ade87c-9f49-46d3-a678-7b22406c7956/dqc_reference
[2023-06-29 20:05:54,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:05:54,498] [INFO] Task started: Prodigal
[2023-06-29 20:05:54,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg491cdb18-4c8a-421e-a9bf-f5c2a6858d67/GCA_021738285.1_ASM2173828v1_genomic.fna.gz | prodigal -d GCA_021738285.1_ASM2173828v1_genomic.fna/cds.fna -a GCA_021738285.1_ASM2173828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:05:56,535] [INFO] Task succeeded: Prodigal
[2023-06-29 20:05:56,535] [INFO] Task started: HMMsearch
[2023-06-29 20:05:56,535] [INFO] Running command: hmmsearch --tblout GCA_021738285.1_ASM2173828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1ade87c-9f49-46d3-a678-7b22406c7956/dqc_reference/reference_markers.hmm GCA_021738285.1_ASM2173828v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:05:56,733] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:05:56,734] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg491cdb18-4c8a-421e-a9bf-f5c2a6858d67/GCA_021738285.1_ASM2173828v1_genomic.fna.gz]
[2023-06-29 20:05:56,747] [INFO] Query marker FASTA was written to GCA_021738285.1_ASM2173828v1_genomic.fna/markers.fasta
[2023-06-29 20:05:56,747] [INFO] Task started: Blastn
[2023-06-29 20:05:56,747] [INFO] Running command: blastn -query GCA_021738285.1_ASM2173828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ade87c-9f49-46d3-a678-7b22406c7956/dqc_reference/reference_markers.fasta -out GCA_021738285.1_ASM2173828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:05:57,339] [INFO] Task succeeded: Blastn
[2023-06-29 20:05:57,343] [INFO] Selected 13 target genomes.
[2023-06-29 20:05:57,343] [INFO] Target genome list was writen to GCA_021738285.1_ASM2173828v1_genomic.fna/target_genomes.txt
[2023-06-29 20:05:57,344] [INFO] Task started: fastANI
[2023-06-29 20:05:57,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg491cdb18-4c8a-421e-a9bf-f5c2a6858d67/GCA_021738285.1_ASM2173828v1_genomic.fna.gz --refList GCA_021738285.1_ASM2173828v1_genomic.fna/target_genomes.txt --output GCA_021738285.1_ASM2173828v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:06:03,269] [INFO] Task succeeded: fastANI
[2023-06-29 20:06:03,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1ade87c-9f49-46d3-a678-7b22406c7956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:06:03,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1ade87c-9f49-46d3-a678-7b22406c7956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:06:03,274] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:06:03,274] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:06:03,274] [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
Methylotenera versatilis	strain=301	GCA_000093025.1	1055487	1055487	type	True	78.468	63	210	95	below_threshold
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	77.361	61	210	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:06:03,276] [INFO] DFAST Taxonomy check result was written to GCA_021738285.1_ASM2173828v1_genomic.fna/tc_result.tsv
[2023-06-29 20:06:03,277] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:06:03,277] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:06:03,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1ade87c-9f49-46d3-a678-7b22406c7956/dqc_reference/checkm_data
[2023-06-29 20:06:03,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:06:03,289] [INFO] Task started: CheckM
[2023-06-29 20:06:03,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021738285.1_ASM2173828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021738285.1_ASM2173828v1_genomic.fna/checkm_input GCA_021738285.1_ASM2173828v1_genomic.fna/checkm_result
[2023-06-29 20:06:17,607] [INFO] Task succeeded: CheckM
[2023-06-29 20:06:17,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:06:17,629] [INFO] ===== Completeness check finished =====
[2023-06-29 20:06:17,629] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:06:17,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021738285.1_ASM2173828v1_genomic.fna/markers.fasta)
[2023-06-29 20:06:17,630] [INFO] Task started: Blastn
[2023-06-29 20:06:17,630] [INFO] Running command: blastn -query GCA_021738285.1_ASM2173828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ade87c-9f49-46d3-a678-7b22406c7956/dqc_reference/reference_markers_gtdb.fasta -out GCA_021738285.1_ASM2173828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:06:18,277] [INFO] Task succeeded: Blastn
[2023-06-29 20:06:18,282] [INFO] Selected 8 target genomes.
[2023-06-29 20:06:18,283] [INFO] Target genome list was writen to GCA_021738285.1_ASM2173828v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:06:18,284] [INFO] Task started: fastANI
[2023-06-29 20:06:18,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg491cdb18-4c8a-421e-a9bf-f5c2a6858d67/GCA_021738285.1_ASM2173828v1_genomic.fna.gz --refList GCA_021738285.1_ASM2173828v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021738285.1_ASM2173828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:06:21,067] [INFO] Task succeeded: fastANI
[2023-06-29 20:06:21,078] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:06:21,079] [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_903951385.1	s__Methylotenera sp903951385	96.0288	139	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	97.55	95.40	0.76	0.67	13	conclusive
GCA_005777825.1	s__Methylotenera sp005777825	93.0926	173	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.74	99.74	0.93	0.93	2	-
GCA_005791685.1	s__Methylotenera sp005791685	83.279	150	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.44	99.44	0.86	0.86	2	-
GCA_903833595.1	s__Methylotenera sp903833595	78.6947	73	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	97.98	97.98	0.85	0.85	2	-
GCA_903876765.1	s__Methylotenera sp903876765	78.4056	92	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.98	99.97	0.97	0.96	3	-
GCA_013141495.1	s__Methylotenera sp013141495	77.9082	55	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	98.86	98.86	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-29 20:06:21,081] [INFO] GTDB search result was written to GCA_021738285.1_ASM2173828v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:06:21,082] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:06:21,086] [INFO] DFAST_QC result json was written to GCA_021738285.1_ASM2173828v1_genomic.fna/dqc_result.json
[2023-06-29 20:06:21,086] [INFO] DFAST_QC completed!
[2023-06-29 20:06:21,086] [INFO] Total running time: 0h0m28s