[2023-06-13 13:00:23,171] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:00:23,174] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:00:23,174] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6db3c52-62df-4ac0-9765-95421a7c400e/dqc_reference
[2023-06-13 13:00:24,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:00:24,410] [INFO] Task started: Prodigal
[2023-06-13 13:00:24,410] [INFO] Running command: gunzip -c /var/lib/cwl/stgb50ad530-29b1-439c-a5c7-1bd29940fdcb/GCA_947855985.1_chick17_bin14_genomic.fna.gz | prodigal -d GCA_947855985.1_chick17_bin14_genomic.fna/cds.fna -a GCA_947855985.1_chick17_bin14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:00:25,802] [INFO] Task succeeded: Prodigal
[2023-06-13 13:00:25,802] [INFO] Task started: HMMsearch
[2023-06-13 13:00:25,803] [INFO] Running command: hmmsearch --tblout GCA_947855985.1_chick17_bin14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6db3c52-62df-4ac0-9765-95421a7c400e/dqc_reference/reference_markers.hmm GCA_947855985.1_chick17_bin14_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:00:26,027] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:00:26,029] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb50ad530-29b1-439c-a5c7-1bd29940fdcb/GCA_947855985.1_chick17_bin14_genomic.fna.gz]
[2023-06-13 13:00:26,048] [INFO] Query marker FASTA was written to GCA_947855985.1_chick17_bin14_genomic.fna/markers.fasta
[2023-06-13 13:00:26,048] [INFO] Task started: Blastn
[2023-06-13 13:00:26,048] [INFO] Running command: blastn -query GCA_947855985.1_chick17_bin14_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6db3c52-62df-4ac0-9765-95421a7c400e/dqc_reference/reference_markers.fasta -out GCA_947855985.1_chick17_bin14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:26,617] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:26,621] [INFO] Selected 26 target genomes.
[2023-06-13 13:00:26,621] [INFO] Target genome list was writen to GCA_947855985.1_chick17_bin14_genomic.fna/target_genomes.txt
[2023-06-13 13:00:26,625] [INFO] Task started: fastANI
[2023-06-13 13:00:26,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgb50ad530-29b1-439c-a5c7-1bd29940fdcb/GCA_947855985.1_chick17_bin14_genomic.fna.gz --refList GCA_947855985.1_chick17_bin14_genomic.fna/target_genomes.txt --output GCA_947855985.1_chick17_bin14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:00:36,380] [INFO] Task succeeded: fastANI
[2023-06-13 13:00:36,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6db3c52-62df-4ac0-9765-95421a7c400e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:00:36,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6db3c52-62df-4ac0-9765-95421a7c400e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:00:36,383] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:00:36,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 13:00:36,384] [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
--------------------------------------------------------------------------------
[2023-06-13 13:00:36,386] [INFO] DFAST Taxonomy check result was written to GCA_947855985.1_chick17_bin14_genomic.fna/tc_result.tsv
[2023-06-13 13:00:36,387] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:00:36,387] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:00:36,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6db3c52-62df-4ac0-9765-95421a7c400e/dqc_reference/checkm_data
[2023-06-13 13:00:36,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:00:36,409] [INFO] Task started: CheckM
[2023-06-13 13:00:36,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947855985.1_chick17_bin14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947855985.1_chick17_bin14_genomic.fna/checkm_input GCA_947855985.1_chick17_bin14_genomic.fna/checkm_result
[2023-06-13 13:00:49,581] [INFO] Task succeeded: CheckM
[2023-06-13 13:00:49,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 2.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 13:00:49,604] [INFO] ===== Completeness check finished =====
[2023-06-13 13:00:49,604] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:00:49,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947855985.1_chick17_bin14_genomic.fna/markers.fasta)
[2023-06-13 13:00:49,605] [INFO] Task started: Blastn
[2023-06-13 13:00:49,605] [INFO] Running command: blastn -query GCA_947855985.1_chick17_bin14_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6db3c52-62df-4ac0-9765-95421a7c400e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947855985.1_chick17_bin14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:50,439] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:50,445] [INFO] Selected 28 target genomes.
[2023-06-13 13:00:50,445] [INFO] Target genome list was writen to GCA_947855985.1_chick17_bin14_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:00:50,454] [INFO] Task started: fastANI
[2023-06-13 13:00:50,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgb50ad530-29b1-439c-a5c7-1bd29940fdcb/GCA_947855985.1_chick17_bin14_genomic.fna.gz --refList GCA_947855985.1_chick17_bin14_genomic.fna/target_genomes_gtdb.txt --output GCA_947855985.1_chick17_bin14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:00:58,150] [INFO] Task succeeded: fastANI
[2023-06-13 13:00:58,160] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:00:58,161] [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_017435255.1	s__RGIG3091 sp017435255	79.6844	118	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG3091	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436345.1	s__RUG11788 sp017436345	78.0002	66	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432595.1	s__CAG-710 sp000432595	77.9959	56	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-710	95.0	98.45	98.40	0.90	0.89	3	-
GCA_015059405.1	s__RUG11788 sp015059405	77.3163	70	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625395.1	s__RUG13868 sp017625395	77.1348	63	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295795.1	s__CAG-710 sp016295795	77.1346	54	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-710	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:00:58,163] [INFO] GTDB search result was written to GCA_947855985.1_chick17_bin14_genomic.fna/result_gtdb.tsv
[2023-06-13 13:00:58,163] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:00:58,168] [INFO] DFAST_QC result json was written to GCA_947855985.1_chick17_bin14_genomic.fna/dqc_result.json
[2023-06-13 13:00:58,168] [INFO] DFAST_QC completed!
[2023-06-13 13:00:58,168] [INFO] Total running time: 0h0m35s