[2023-06-04 18:26:16,663] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:26:16,671] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:26:16,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg767024f2-052f-4ab8-a6bc-122236b80d82/dqc_reference
[2023-06-04 18:26:19,519] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:26:19,519] [INFO] Task started: Prodigal
[2023-06-04 18:26:19,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf44852b-ddda-41ba-ad9a-23d853835069/GCA_934438045.1_ERR7738269_bin.8_genomic.fna.gz | prodigal -d GCA_934438045.1_ERR7738269_bin.8_genomic.fna/cds.fna -a GCA_934438045.1_ERR7738269_bin.8_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:26:23,857] [INFO] Task succeeded: Prodigal
[2023-06-04 18:26:23,857] [INFO] Task started: HMMsearch
[2023-06-04 18:26:23,858] [INFO] Running command: hmmsearch --tblout GCA_934438045.1_ERR7738269_bin.8_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg767024f2-052f-4ab8-a6bc-122236b80d82/dqc_reference/reference_markers.hmm GCA_934438045.1_ERR7738269_bin.8_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:26:24,074] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:26:24,075] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbf44852b-ddda-41ba-ad9a-23d853835069/GCA_934438045.1_ERR7738269_bin.8_genomic.fna.gz]
[2023-06-04 18:26:24,095] [INFO] Query marker FASTA was written to GCA_934438045.1_ERR7738269_bin.8_genomic.fna/markers.fasta
[2023-06-04 18:26:24,096] [INFO] Task started: Blastn
[2023-06-04 18:26:24,096] [INFO] Running command: blastn -query GCA_934438045.1_ERR7738269_bin.8_genomic.fna/markers.fasta -db /var/lib/cwl/stg767024f2-052f-4ab8-a6bc-122236b80d82/dqc_reference/reference_markers.fasta -out GCA_934438045.1_ERR7738269_bin.8_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:26:24,688] [INFO] Task succeeded: Blastn
[2023-06-04 18:26:24,692] [INFO] Selected 20 target genomes.
[2023-06-04 18:26:24,692] [INFO] Target genome list was writen to GCA_934438045.1_ERR7738269_bin.8_genomic.fna/target_genomes.txt
[2023-06-04 18:26:24,786] [INFO] Task started: fastANI
[2023-06-04 18:26:24,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf44852b-ddda-41ba-ad9a-23d853835069/GCA_934438045.1_ERR7738269_bin.8_genomic.fna.gz --refList GCA_934438045.1_ERR7738269_bin.8_genomic.fna/target_genomes.txt --output GCA_934438045.1_ERR7738269_bin.8_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:26:34,877] [INFO] Task succeeded: fastANI
[2023-06-04 18:26:34,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg767024f2-052f-4ab8-a6bc-122236b80d82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:26:34,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg767024f2-052f-4ab8-a6bc-122236b80d82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:26:34,880] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:26:34,881] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:26:34,881] [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
--------------------------------------------------------------------------------
[2023-06-04 18:26:34,883] [INFO] DFAST Taxonomy check result was written to GCA_934438045.1_ERR7738269_bin.8_genomic.fna/tc_result.tsv
[2023-06-04 18:26:34,883] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:26:34,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:26:34,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg767024f2-052f-4ab8-a6bc-122236b80d82/dqc_reference/checkm_data
[2023-06-04 18:26:34,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:26:34,909] [INFO] Task started: CheckM
[2023-06-04 18:26:34,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934438045.1_ERR7738269_bin.8_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934438045.1_ERR7738269_bin.8_genomic.fna/checkm_input GCA_934438045.1_ERR7738269_bin.8_genomic.fna/checkm_result
[2023-06-04 18:26:54,726] [INFO] Task succeeded: CheckM
[2023-06-04 18:26:54,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:26:54,749] [INFO] ===== Completeness check finished =====
[2023-06-04 18:26:54,750] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:26:54,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934438045.1_ERR7738269_bin.8_genomic.fna/markers.fasta)
[2023-06-04 18:26:54,751] [INFO] Task started: Blastn
[2023-06-04 18:26:54,751] [INFO] Running command: blastn -query GCA_934438045.1_ERR7738269_bin.8_genomic.fna/markers.fasta -db /var/lib/cwl/stg767024f2-052f-4ab8-a6bc-122236b80d82/dqc_reference/reference_markers_gtdb.fasta -out GCA_934438045.1_ERR7738269_bin.8_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:26:55,626] [INFO] Task succeeded: Blastn
[2023-06-04 18:26:55,630] [INFO] Selected 21 target genomes.
[2023-06-04 18:26:55,630] [INFO] Target genome list was writen to GCA_934438045.1_ERR7738269_bin.8_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:26:55,946] [INFO] Task started: fastANI
[2023-06-04 18:26:55,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf44852b-ddda-41ba-ad9a-23d853835069/GCA_934438045.1_ERR7738269_bin.8_genomic.fna.gz --refList GCA_934438045.1_ERR7738269_bin.8_genomic.fna/target_genomes_gtdb.txt --output GCA_934438045.1_ERR7738269_bin.8_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:27:02,784] [INFO] Task succeeded: fastANI
[2023-06-04 18:27:02,787] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:27:02,787] [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_004558975.1	s__UBA1740 sp004558975	97.4881	265	461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740	95.0	97.93	97.93	0.93	0.93	2	conclusive
--------------------------------------------------------------------------------
[2023-06-04 18:27:02,789] [INFO] GTDB search result was written to GCA_934438045.1_ERR7738269_bin.8_genomic.fna/result_gtdb.tsv
[2023-06-04 18:27:02,789] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:27:02,792] [INFO] DFAST_QC result json was written to GCA_934438045.1_ERR7738269_bin.8_genomic.fna/dqc_result.json
[2023-06-04 18:27:02,792] [INFO] DFAST_QC completed!
[2023-06-04 18:27:02,792] [INFO] Total running time: 0h0m46s