[2023-06-30 14:11:23,277] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:11:23,279] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:11:23,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg452a73ce-bac5-4288-809c-ea06283b1ca0/dqc_reference
[2023-06-30 14:11:24,466] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:11:24,467] [INFO] Task started: Prodigal
[2023-06-30 14:11:24,467] [INFO] Running command: gunzip -c /var/lib/cwl/stge55f8edf-089b-4b99-8b0e-c2c803cf2dad/GCA_900764635.1_SRS2320657_6_genomic.fna.gz | prodigal -d GCA_900764635.1_SRS2320657_6_genomic.fna/cds.fna -a GCA_900764635.1_SRS2320657_6_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:11:27,292] [INFO] Task succeeded: Prodigal
[2023-06-30 14:11:27,293] [INFO] Task started: HMMsearch
[2023-06-30 14:11:27,293] [INFO] Running command: hmmsearch --tblout GCA_900764635.1_SRS2320657_6_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg452a73ce-bac5-4288-809c-ea06283b1ca0/dqc_reference/reference_markers.hmm GCA_900764635.1_SRS2320657_6_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:11:27,492] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:11:27,493] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge55f8edf-089b-4b99-8b0e-c2c803cf2dad/GCA_900764635.1_SRS2320657_6_genomic.fna.gz]
[2023-06-30 14:11:27,515] [INFO] Query marker FASTA was written to GCA_900764635.1_SRS2320657_6_genomic.fna/markers.fasta
[2023-06-30 14:11:27,516] [INFO] Task started: Blastn
[2023-06-30 14:11:27,516] [INFO] Running command: blastn -query GCA_900764635.1_SRS2320657_6_genomic.fna/markers.fasta -db /var/lib/cwl/stg452a73ce-bac5-4288-809c-ea06283b1ca0/dqc_reference/reference_markers.fasta -out GCA_900764635.1_SRS2320657_6_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:11:28,127] [INFO] Task succeeded: Blastn
[2023-06-30 14:11:28,132] [INFO] Selected 24 target genomes.
[2023-06-30 14:11:28,133] [INFO] Target genome list was writen to GCA_900764635.1_SRS2320657_6_genomic.fna/target_genomes.txt
[2023-06-30 14:11:28,155] [INFO] Task started: fastANI
[2023-06-30 14:11:28,156] [INFO] Running command: fastANI --query /var/lib/cwl/stge55f8edf-089b-4b99-8b0e-c2c803cf2dad/GCA_900764635.1_SRS2320657_6_genomic.fna.gz --refList GCA_900764635.1_SRS2320657_6_genomic.fna/target_genomes.txt --output GCA_900764635.1_SRS2320657_6_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:11:40,187] [INFO] Task succeeded: fastANI
[2023-06-30 14:11:40,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg452a73ce-bac5-4288-809c-ea06283b1ca0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:11:40,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg452a73ce-bac5-4288-809c-ea06283b1ca0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:11:40,195] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 14:11:40,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 14:11:40,196] [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
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	96.1212	54	92	95	conclusive
--------------------------------------------------------------------------------
[2023-06-30 14:11:40,198] [INFO] DFAST Taxonomy check result was written to GCA_900764635.1_SRS2320657_6_genomic.fna/tc_result.tsv
[2023-06-30 14:11:40,199] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:11:40,199] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:11:40,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg452a73ce-bac5-4288-809c-ea06283b1ca0/dqc_reference/checkm_data
[2023-06-30 14:11:40,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:11:40,227] [INFO] Task started: CheckM
[2023-06-30 14:11:40,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900764635.1_SRS2320657_6_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900764635.1_SRS2320657_6_genomic.fna/checkm_input GCA_900764635.1_SRS2320657_6_genomic.fna/checkm_result
[2023-06-30 14:11:56,504] [INFO] Task succeeded: CheckM
[2023-06-30 14:11:56,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:11:56,524] [INFO] ===== Completeness check finished =====
[2023-06-30 14:11:56,525] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:11:56,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900764635.1_SRS2320657_6_genomic.fna/markers.fasta)
[2023-06-30 14:11:56,525] [INFO] Task started: Blastn
[2023-06-30 14:11:56,526] [INFO] Running command: blastn -query GCA_900764635.1_SRS2320657_6_genomic.fna/markers.fasta -db /var/lib/cwl/stg452a73ce-bac5-4288-809c-ea06283b1ca0/dqc_reference/reference_markers_gtdb.fasta -out GCA_900764635.1_SRS2320657_6_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:11:57,434] [INFO] Task succeeded: Blastn
[2023-06-30 14:11:57,439] [INFO] Selected 14 target genomes.
[2023-06-30 14:11:57,439] [INFO] Target genome list was writen to GCA_900764635.1_SRS2320657_6_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:11:57,444] [INFO] Task started: fastANI
[2023-06-30 14:11:57,444] [INFO] Running command: fastANI --query /var/lib/cwl/stge55f8edf-089b-4b99-8b0e-c2c803cf2dad/GCA_900764635.1_SRS2320657_6_genomic.fna.gz --refList GCA_900764635.1_SRS2320657_6_genomic.fna/target_genomes_gtdb.txt --output GCA_900764635.1_SRS2320657_6_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:12:03,979] [INFO] Task succeeded: fastANI
[2023-06-30 14:12:03,987] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:12:03,987] [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_000332875.2	s__Anaerostipes hadrus	96.1212	54	92	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.35	97.09	0.85	0.65	78	conclusive
GCA_902362875.1	s__Anaerostipes sp900066705	88.0608	54	92	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.31	0.96	0.92	3	-
GCF_001404655.1	s__Anaerostipes hadrus_A	86.963	54	92	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.11	98.66	0.92	0.88	9	-
--------------------------------------------------------------------------------
[2023-06-30 14:12:03,989] [INFO] GTDB search result was written to GCA_900764635.1_SRS2320657_6_genomic.fna/result_gtdb.tsv
[2023-06-30 14:12:03,990] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:12:03,992] [INFO] DFAST_QC result json was written to GCA_900764635.1_SRS2320657_6_genomic.fna/dqc_result.json
[2023-06-30 14:12:03,993] [INFO] DFAST_QC completed!
[2023-06-30 14:12:03,993] [INFO] Total running time: 0h0m41s