[2023-06-29 02:28:50,172] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:28:50,174] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:28:50,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg04864bdf-2f1a-45ba-aa2a-a3fd2549ed1b/dqc_reference
[2023-06-29 02:28:51,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:28:51,860] [INFO] Task started: Prodigal
[2023-06-29 02:28:51,860] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd87adc6-90d1-45e7-97cc-d27c835782a2/GCA_012800335.1_ASM1280033v1_genomic.fna.gz | prodigal -d GCA_012800335.1_ASM1280033v1_genomic.fna/cds.fna -a GCA_012800335.1_ASM1280033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:28:55,278] [INFO] Task succeeded: Prodigal
[2023-06-29 02:28:55,278] [INFO] Task started: HMMsearch
[2023-06-29 02:28:55,278] [INFO] Running command: hmmsearch --tblout GCA_012800335.1_ASM1280033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04864bdf-2f1a-45ba-aa2a-a3fd2549ed1b/dqc_reference/reference_markers.hmm GCA_012800335.1_ASM1280033v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:28:55,516] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:28:55,518] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdd87adc6-90d1-45e7-97cc-d27c835782a2/GCA_012800335.1_ASM1280033v1_genomic.fna.gz]
[2023-06-29 02:28:55,548] [INFO] Query marker FASTA was written to GCA_012800335.1_ASM1280033v1_genomic.fna/markers.fasta
[2023-06-29 02:28:55,549] [INFO] Task started: Blastn
[2023-06-29 02:28:55,549] [INFO] Running command: blastn -query GCA_012800335.1_ASM1280033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04864bdf-2f1a-45ba-aa2a-a3fd2549ed1b/dqc_reference/reference_markers.fasta -out GCA_012800335.1_ASM1280033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:28:56,165] [INFO] Task succeeded: Blastn
[2023-06-29 02:28:56,168] [INFO] Selected 14 target genomes.
[2023-06-29 02:28:56,168] [INFO] Target genome list was writen to GCA_012800335.1_ASM1280033v1_genomic.fna/target_genomes.txt
[2023-06-29 02:28:56,176] [INFO] Task started: fastANI
[2023-06-29 02:28:56,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd87adc6-90d1-45e7-97cc-d27c835782a2/GCA_012800335.1_ASM1280033v1_genomic.fna.gz --refList GCA_012800335.1_ASM1280033v1_genomic.fna/target_genomes.txt --output GCA_012800335.1_ASM1280033v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:29:03,825] [INFO] Task succeeded: fastANI
[2023-06-29 02:29:03,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04864bdf-2f1a-45ba-aa2a-a3fd2549ed1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:29:03,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04864bdf-2f1a-45ba-aa2a-a3fd2549ed1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:29:03,828] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:29:03,828] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 02:29:03,829] [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
--------------------------------------------------------------------------------
[2023-06-29 02:29:03,831] [INFO] DFAST Taxonomy check result was written to GCA_012800335.1_ASM1280033v1_genomic.fna/tc_result.tsv
[2023-06-29 02:29:03,832] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:29:03,832] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:29:03,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04864bdf-2f1a-45ba-aa2a-a3fd2549ed1b/dqc_reference/checkm_data
[2023-06-29 02:29:03,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:29:03,859] [INFO] Task started: CheckM
[2023-06-29 02:29:03,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012800335.1_ASM1280033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012800335.1_ASM1280033v1_genomic.fna/checkm_input GCA_012800335.1_ASM1280033v1_genomic.fna/checkm_result
[2023-06-29 02:29:23,044] [INFO] Task succeeded: CheckM
[2023-06-29 02:29:23,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:29:23,073] [INFO] ===== Completeness check finished =====
[2023-06-29 02:29:23,073] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:29:23,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012800335.1_ASM1280033v1_genomic.fna/markers.fasta)
[2023-06-29 02:29:23,074] [INFO] Task started: Blastn
[2023-06-29 02:29:23,074] [INFO] Running command: blastn -query GCA_012800335.1_ASM1280033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04864bdf-2f1a-45ba-aa2a-a3fd2549ed1b/dqc_reference/reference_markers_gtdb.fasta -out GCA_012800335.1_ASM1280033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:29:23,860] [INFO] Task succeeded: Blastn
[2023-06-29 02:29:23,864] [INFO] Selected 12 target genomes.
[2023-06-29 02:29:23,864] [INFO] Target genome list was writen to GCA_012800335.1_ASM1280033v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:29:23,868] [INFO] Task started: fastANI
[2023-06-29 02:29:23,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd87adc6-90d1-45e7-97cc-d27c835782a2/GCA_012800335.1_ASM1280033v1_genomic.fna.gz --refList GCA_012800335.1_ASM1280033v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012800335.1_ASM1280033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:29:29,733] [INFO] Task succeeded: fastANI
[2023-06-29 02:29:29,738] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 02:29:29,738] [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_012839235.1	s__Mobilitalea sp012839235	84.6975	307	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523925.1	s__Mobilitalea sp012523925	76.321	60	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 02:29:29,741] [INFO] GTDB search result was written to GCA_012800335.1_ASM1280033v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:29:29,741] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:29:29,744] [INFO] DFAST_QC result json was written to GCA_012800335.1_ASM1280033v1_genomic.fna/dqc_result.json
[2023-06-29 02:29:29,744] [INFO] DFAST_QC completed!
[2023-06-29 02:29:29,744] [INFO] Total running time: 0h0m40s