[2023-06-13 09:11:57,247] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:11:57,249] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:11:57,249] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc9690d0-47a4-42fe-890f-3f2f95dc0ef9/dqc_reference
[2023-06-13 09:11:58,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:11:58,594] [INFO] Task started: Prodigal
[2023-06-13 09:11:58,594] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0201997-fd52-42d3-9cae-6e126eb8b022/GCA_947482985.1_TE-Jun18-39_genomic.fna.gz | prodigal -d GCA_947482985.1_TE-Jun18-39_genomic.fna/cds.fna -a GCA_947482985.1_TE-Jun18-39_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:12:02,323] [INFO] Task succeeded: Prodigal
[2023-06-13 09:12:02,323] [INFO] Task started: HMMsearch
[2023-06-13 09:12:02,324] [INFO] Running command: hmmsearch --tblout GCA_947482985.1_TE-Jun18-39_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc9690d0-47a4-42fe-890f-3f2f95dc0ef9/dqc_reference/reference_markers.hmm GCA_947482985.1_TE-Jun18-39_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:12:02,605] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:12:02,606] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc0201997-fd52-42d3-9cae-6e126eb8b022/GCA_947482985.1_TE-Jun18-39_genomic.fna.gz]
[2023-06-13 09:12:02,631] [INFO] Query marker FASTA was written to GCA_947482985.1_TE-Jun18-39_genomic.fna/markers.fasta
[2023-06-13 09:12:02,632] [INFO] Task started: Blastn
[2023-06-13 09:12:02,632] [INFO] Running command: blastn -query GCA_947482985.1_TE-Jun18-39_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc9690d0-47a4-42fe-890f-3f2f95dc0ef9/dqc_reference/reference_markers.fasta -out GCA_947482985.1_TE-Jun18-39_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:03,235] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:03,238] [INFO] Selected 16 target genomes.
[2023-06-13 09:12:03,239] [INFO] Target genome list was writen to GCA_947482985.1_TE-Jun18-39_genomic.fna/target_genomes.txt
[2023-06-13 09:12:03,244] [INFO] Task started: fastANI
[2023-06-13 09:12:03,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0201997-fd52-42d3-9cae-6e126eb8b022/GCA_947482985.1_TE-Jun18-39_genomic.fna.gz --refList GCA_947482985.1_TE-Jun18-39_genomic.fna/target_genomes.txt --output GCA_947482985.1_TE-Jun18-39_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:13,758] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:13,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc9690d0-47a4-42fe-890f-3f2f95dc0ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:13,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc9690d0-47a4-42fe-890f-3f2f95dc0ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:13,762] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:12:13,762] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 09:12:13,762] [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 09:12:13,768] [INFO] DFAST Taxonomy check result was written to GCA_947482985.1_TE-Jun18-39_genomic.fna/tc_result.tsv
[2023-06-13 09:12:13,769] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:13,769] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:13,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc9690d0-47a4-42fe-890f-3f2f95dc0ef9/dqc_reference/checkm_data
[2023-06-13 09:12:13,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:13,792] [INFO] Task started: CheckM
[2023-06-13 09:12:13,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947482985.1_TE-Jun18-39_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947482985.1_TE-Jun18-39_genomic.fna/checkm_input GCA_947482985.1_TE-Jun18-39_genomic.fna/checkm_result
[2023-06-13 09:12:34,807] [INFO] Task succeeded: CheckM
[2023-06-13 09:12:34,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:12:34,850] [INFO] ===== Completeness check finished =====
[2023-06-13 09:12:34,850] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:12:34,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947482985.1_TE-Jun18-39_genomic.fna/markers.fasta)
[2023-06-13 09:12:34,852] [INFO] Task started: Blastn
[2023-06-13 09:12:34,852] [INFO] Running command: blastn -query GCA_947482985.1_TE-Jun18-39_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc9690d0-47a4-42fe-890f-3f2f95dc0ef9/dqc_reference/reference_markers_gtdb.fasta -out GCA_947482985.1_TE-Jun18-39_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:35,716] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:35,722] [INFO] Selected 10 target genomes.
[2023-06-13 09:12:35,722] [INFO] Target genome list was writen to GCA_947482985.1_TE-Jun18-39_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:12:35,729] [INFO] Task started: fastANI
[2023-06-13 09:12:35,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0201997-fd52-42d3-9cae-6e126eb8b022/GCA_947482985.1_TE-Jun18-39_genomic.fna.gz --refList GCA_947482985.1_TE-Jun18-39_genomic.fna/target_genomes_gtdb.txt --output GCA_947482985.1_TE-Jun18-39_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:12:40,071] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:40,081] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 09:12:40,082] [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_903961015.1	s__F1-60-MAGs104 sp903961015	94.0595	293	326	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	99.31	98.85	0.88	0.85	12	-
GCA_005792145.1	s__F1-60-MAGs104 sp005792145	88.0116	285	326	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	99.70	99.55	0.92	0.92	5	-
GCA_903919715.1	s__F1-60-MAGs104 sp903919715	80.6592	214	326	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	99.88	99.87	0.97	0.95	5	-
--------------------------------------------------------------------------------
[2023-06-13 09:12:40,085] [INFO] GTDB search result was written to GCA_947482985.1_TE-Jun18-39_genomic.fna/result_gtdb.tsv
[2023-06-13 09:12:40,086] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:12:40,089] [INFO] DFAST_QC result json was written to GCA_947482985.1_TE-Jun18-39_genomic.fna/dqc_result.json
[2023-06-13 09:12:40,090] [INFO] DFAST_QC completed!
[2023-06-13 09:12:40,090] [INFO] Total running time: 0h0m43s