[2023-06-17 05:49:17,990] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:49:17,993] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:49:17,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b48c457-b573-4a8c-9ad7-64b67c2d3174/dqc_reference
[2023-06-17 05:49:20,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:49:20,245] [INFO] Task started: Prodigal
[2023-06-17 05:49:20,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg731d499b-4777-4a5a-8305-a058daec4720/GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna.gz | prodigal -d GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/cds.fna -a GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:49:22,777] [INFO] Task succeeded: Prodigal
[2023-06-17 05:49:22,778] [INFO] Task started: HMMsearch
[2023-06-17 05:49:22,778] [INFO] Running command: hmmsearch --tblout GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b48c457-b573-4a8c-9ad7-64b67c2d3174/dqc_reference/reference_markers.hmm GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:49:23,013] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:49:23,015] [INFO] Found 6/6 markers.
[2023-06-17 05:49:23,034] [INFO] Query marker FASTA was written to GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/markers.fasta
[2023-06-17 05:49:23,035] [INFO] Task started: Blastn
[2023-06-17 05:49:23,035] [INFO] Running command: blastn -query GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b48c457-b573-4a8c-9ad7-64b67c2d3174/dqc_reference/reference_markers.fasta -out GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:49:24,295] [INFO] Task succeeded: Blastn
[2023-06-17 05:49:24,299] [INFO] Selected 28 target genomes.
[2023-06-17 05:49:24,300] [INFO] Target genome list was writen to GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/target_genomes.txt
[2023-06-17 05:49:24,365] [INFO] Task started: fastANI
[2023-06-17 05:49:24,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg731d499b-4777-4a5a-8305-a058daec4720/GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna.gz --refList GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/target_genomes.txt --output GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 05:49:40,037] [INFO] Task succeeded: fastANI
[2023-06-17 05:49:40,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b48c457-b573-4a8c-9ad7-64b67c2d3174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 05:49:40,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b48c457-b573-4a8c-9ad7-64b67c2d3174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 05:49:40,041] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 05:49:40,041] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 05:49:40,041] [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
--------------------------------------------------------------------------------
[2023-06-17 05:49:40,044] [INFO] DFAST Taxonomy check result was written to GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/tc_result.tsv
[2023-06-17 05:49:40,045] [INFO] ===== Taxonomy check completed =====
[2023-06-17 05:49:40,045] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 05:49:40,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b48c457-b573-4a8c-9ad7-64b67c2d3174/dqc_reference/checkm_data
[2023-06-17 05:49:40,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 05:49:40,067] [INFO] Task started: CheckM
[2023-06-17 05:49:40,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/checkm_input GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/checkm_result
[2023-06-17 05:49:55,296] [INFO] Task succeeded: CheckM
[2023-06-17 05:49:55,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 05:49:55,319] [INFO] ===== Completeness check finished =====
[2023-06-17 05:49:55,320] [INFO] ===== Start GTDB Search =====
[2023-06-17 05:49:55,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/markers.fasta)
[2023-06-17 05:49:55,320] [INFO] Task started: Blastn
[2023-06-17 05:49:55,320] [INFO] Running command: blastn -query GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b48c457-b573-4a8c-9ad7-64b67c2d3174/dqc_reference/reference_markers_gtdb.fasta -out GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:49:56,080] [INFO] Task succeeded: Blastn
[2023-06-17 05:49:56,084] [INFO] Selected 29 target genomes.
[2023-06-17 05:49:56,084] [INFO] Target genome list was writen to GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 05:49:56,124] [INFO] Task started: fastANI
[2023-06-17 05:49:56,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg731d499b-4777-4a5a-8305-a058daec4720/GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna.gz --refList GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/target_genomes_gtdb.txt --output GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:50:05,830] [INFO] Task succeeded: fastANI
[2023-06-17 05:50:05,835] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 05:50:05,835] [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_004558105.1	s__SFEB01 sp004558105	97.0551	272	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__SFEB01	95.0	97.80	97.16	0.85	0.80	9	conclusive
--------------------------------------------------------------------------------
[2023-06-17 05:50:05,837] [INFO] GTDB search result was written to GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/result_gtdb.tsv
[2023-06-17 05:50:05,839] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:50:05,867] [INFO] DFAST_QC result json was written to GCA_905199065.1_ERR414351-mag-bin.18_genomic.fna/dqc_result.json
[2023-06-17 05:50:05,867] [INFO] DFAST_QC completed!
[2023-06-17 05:50:05,868] [INFO] Total running time: 0h0m48s