[2023-06-28 12:29:17,676] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:29:17,679] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:29:17,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg36b4b3a7-1c68-4bc2-a6f7-c1b004b2acc5/dqc_reference
[2023-06-28 12:29:19,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:29:19,933] [INFO] Task started: Prodigal
[2023-06-28 12:29:19,933] [INFO] Running command: gunzip -c /var/lib/cwl/stgb592acf9-38d5-46cb-867b-51cc6fe04a9f/GCA_005791285.1_ASM579128v1_genomic.fna.gz | prodigal -d GCA_005791285.1_ASM579128v1_genomic.fna/cds.fna -a GCA_005791285.1_ASM579128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:29:23,096] [INFO] Task succeeded: Prodigal
[2023-06-28 12:29:23,096] [INFO] Task started: HMMsearch
[2023-06-28 12:29:23,097] [INFO] Running command: hmmsearch --tblout GCA_005791285.1_ASM579128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36b4b3a7-1c68-4bc2-a6f7-c1b004b2acc5/dqc_reference/reference_markers.hmm GCA_005791285.1_ASM579128v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:29:23,267] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:29:23,269] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgb592acf9-38d5-46cb-867b-51cc6fe04a9f/GCA_005791285.1_ASM579128v1_genomic.fna.gz]
[2023-06-28 12:29:23,289] [INFO] Query marker FASTA was written to GCA_005791285.1_ASM579128v1_genomic.fna/markers.fasta
[2023-06-28 12:29:23,289] [INFO] Task started: Blastn
[2023-06-28 12:29:23,289] [INFO] Running command: blastn -query GCA_005791285.1_ASM579128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36b4b3a7-1c68-4bc2-a6f7-c1b004b2acc5/dqc_reference/reference_markers.fasta -out GCA_005791285.1_ASM579128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:29:24,436] [INFO] Task succeeded: Blastn
[2023-06-28 12:29:24,440] [INFO] Selected 5 target genomes.
[2023-06-28 12:29:24,441] [INFO] Target genome list was writen to GCA_005791285.1_ASM579128v1_genomic.fna/target_genomes.txt
[2023-06-28 12:29:24,444] [INFO] Task started: fastANI
[2023-06-28 12:29:24,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgb592acf9-38d5-46cb-867b-51cc6fe04a9f/GCA_005791285.1_ASM579128v1_genomic.fna.gz --refList GCA_005791285.1_ASM579128v1_genomic.fna/target_genomes.txt --output GCA_005791285.1_ASM579128v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:29:27,624] [INFO] Task succeeded: fastANI
[2023-06-28 12:29:27,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36b4b3a7-1c68-4bc2-a6f7-c1b004b2acc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:29:27,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36b4b3a7-1c68-4bc2-a6f7-c1b004b2acc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:29:27,626] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:29:27,626] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:29:27,626] [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
--------------------------------------------------------------------------------
[2023-06-28 12:29:27,628] [INFO] DFAST Taxonomy check result was written to GCA_005791285.1_ASM579128v1_genomic.fna/tc_result.tsv
[2023-06-28 12:29:27,629] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:29:27,629] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:29:27,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36b4b3a7-1c68-4bc2-a6f7-c1b004b2acc5/dqc_reference/checkm_data
[2023-06-28 12:29:27,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:29:27,651] [INFO] Task started: CheckM
[2023-06-28 12:29:27,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005791285.1_ASM579128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005791285.1_ASM579128v1_genomic.fna/checkm_input GCA_005791285.1_ASM579128v1_genomic.fna/checkm_result
[2023-06-28 12:29:44,815] [INFO] Task succeeded: CheckM
[2023-06-28 12:29:44,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:29:44,838] [INFO] ===== Completeness check finished =====
[2023-06-28 12:29:44,839] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:29:44,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005791285.1_ASM579128v1_genomic.fna/markers.fasta)
[2023-06-28 12:29:44,839] [INFO] Task started: Blastn
[2023-06-28 12:29:44,840] [INFO] Running command: blastn -query GCA_005791285.1_ASM579128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36b4b3a7-1c68-4bc2-a6f7-c1b004b2acc5/dqc_reference/reference_markers_gtdb.fasta -out GCA_005791285.1_ASM579128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:29:45,293] [INFO] Task succeeded: Blastn
[2023-06-28 12:29:45,299] [INFO] Selected 5 target genomes.
[2023-06-28 12:29:45,299] [INFO] Target genome list was writen to GCA_005791285.1_ASM579128v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:29:45,303] [INFO] Task started: fastANI
[2023-06-28 12:29:45,303] [INFO] Running command: fastANI --query /var/lib/cwl/stgb592acf9-38d5-46cb-867b-51cc6fe04a9f/GCA_005791285.1_ASM579128v1_genomic.fna.gz --refList GCA_005791285.1_ASM579128v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005791285.1_ASM579128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:29:48,150] [INFO] Task succeeded: fastANI
[2023-06-28 12:29:48,161] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:29:48,162] [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_903837555.1	s__Rhizomicrobium sp903837555	99.116	283	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013697055.1	s__Rhizomicrobium sp013697055	79.9365	200	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018449595.1	s__Rhizomicrobium sp018449595	79.8918	198	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825865.1	s__Rhizomicrobium sp902825865	79.7355	206	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903857685.1	s__Rhizomicrobium sp903857685	77.2451	100	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	99.22	99.01	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-28 12:29:48,164] [INFO] GTDB search result was written to GCA_005791285.1_ASM579128v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:29:48,165] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:29:48,167] [INFO] DFAST_QC result json was written to GCA_005791285.1_ASM579128v1_genomic.fna/dqc_result.json
[2023-06-28 12:29:48,168] [INFO] DFAST_QC completed!
[2023-06-28 12:29:48,168] [INFO] Total running time: 0h0m30s