[2023-06-17 02:01:53,334] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:01:53,338] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:01:53,338] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4168bd5-64e1-415c-b574-a0d0bd073cdc/dqc_reference
[2023-06-17 02:01:54,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:01:54,898] [INFO] Task started: Prodigal
[2023-06-17 02:01:54,898] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdf4ea4e-6184-4b58-a0f7-c126cd84491b/GCA_003136435.1_20111000_E3D_genomic.fna.gz | prodigal -d GCA_003136435.1_20111000_E3D_genomic.fna/cds.fna -a GCA_003136435.1_20111000_E3D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:01:59,204] [INFO] Task succeeded: Prodigal
[2023-06-17 02:01:59,205] [INFO] Task started: HMMsearch
[2023-06-17 02:01:59,205] [INFO] Running command: hmmsearch --tblout GCA_003136435.1_20111000_E3D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4168bd5-64e1-415c-b574-a0d0bd073cdc/dqc_reference/reference_markers.hmm GCA_003136435.1_20111000_E3D_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:01:59,536] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:01:59,537] [INFO] Found 6/6 markers.
[2023-06-17 02:01:59,585] [INFO] Query marker FASTA was written to GCA_003136435.1_20111000_E3D_genomic.fna/markers.fasta
[2023-06-17 02:01:59,586] [INFO] Task started: Blastn
[2023-06-17 02:01:59,586] [INFO] Running command: blastn -query GCA_003136435.1_20111000_E3D_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4168bd5-64e1-415c-b574-a0d0bd073cdc/dqc_reference/reference_markers.fasta -out GCA_003136435.1_20111000_E3D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:02:00,289] [INFO] Task succeeded: Blastn
[2023-06-17 02:02:00,295] [INFO] Selected 25 target genomes.
[2023-06-17 02:02:00,295] [INFO] Target genome list was writen to GCA_003136435.1_20111000_E3D_genomic.fna/target_genomes.txt
[2023-06-17 02:02:00,324] [INFO] Task started: fastANI
[2023-06-17 02:02:00,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdf4ea4e-6184-4b58-a0f7-c126cd84491b/GCA_003136435.1_20111000_E3D_genomic.fna.gz --refList GCA_003136435.1_20111000_E3D_genomic.fna/target_genomes.txt --output GCA_003136435.1_20111000_E3D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:02:21,939] [INFO] Task succeeded: fastANI
[2023-06-17 02:02:21,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4168bd5-64e1-415c-b574-a0d0bd073cdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:02:21,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4168bd5-64e1-415c-b574-a0d0bd073cdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:02:21,942] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:02:21,942] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:02:21,942] [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 02:02:21,971] [INFO] DFAST Taxonomy check result was written to GCA_003136435.1_20111000_E3D_genomic.fna/tc_result.tsv
[2023-06-17 02:02:21,971] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:02:21,972] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:02:21,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4168bd5-64e1-415c-b574-a0d0bd073cdc/dqc_reference/checkm_data
[2023-06-17 02:02:21,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:02:22,002] [INFO] Task started: CheckM
[2023-06-17 02:02:22,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003136435.1_20111000_E3D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003136435.1_20111000_E3D_genomic.fna/checkm_input GCA_003136435.1_20111000_E3D_genomic.fna/checkm_result
[2023-06-17 02:02:42,441] [INFO] Task succeeded: CheckM
[2023-06-17 02:02:42,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:02:42,467] [INFO] ===== Completeness check finished =====
[2023-06-17 02:02:42,468] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:02:42,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003136435.1_20111000_E3D_genomic.fna/markers.fasta)
[2023-06-17 02:02:42,469] [INFO] Task started: Blastn
[2023-06-17 02:02:42,469] [INFO] Running command: blastn -query GCA_003136435.1_20111000_E3D_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4168bd5-64e1-415c-b574-a0d0bd073cdc/dqc_reference/reference_markers_gtdb.fasta -out GCA_003136435.1_20111000_E3D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:02:43,342] [INFO] Task succeeded: Blastn
[2023-06-17 02:02:43,346] [INFO] Selected 16 target genomes.
[2023-06-17 02:02:43,346] [INFO] Target genome list was writen to GCA_003136435.1_20111000_E3D_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:02:43,396] [INFO] Task started: fastANI
[2023-06-17 02:02:43,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdf4ea4e-6184-4b58-a0f7-c126cd84491b/GCA_003136435.1_20111000_E3D_genomic.fna.gz --refList GCA_003136435.1_20111000_E3D_genomic.fna/target_genomes_gtdb.txt --output GCA_003136435.1_20111000_E3D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:02:53,010] [INFO] Task succeeded: fastANI
[2023-06-17 02:02:53,017] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:02:53,017] [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_003162635.1	s__Fen-1260 sp003162635	96.5599	382	402	d__Bacteria;p__Bacteroidota;c__UBA10030;o__UBA10030;f__UBA6906;g__Fen-1260	95.0	98.68	96.29	0.96	0.94	9	conclusive
GCA_003161955.1	s__Fen-1273 sp003161955	77.7256	65	402	d__Bacteria;p__Bacteroidota;c__UBA10030;o__UBA10030;f__UBA6906;g__Fen-1273	95.0	99.14	99.04	0.88	0.81	5	-
--------------------------------------------------------------------------------
[2023-06-17 02:02:53,019] [INFO] GTDB search result was written to GCA_003136435.1_20111000_E3D_genomic.fna/result_gtdb.tsv
[2023-06-17 02:02:53,020] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:02:53,022] [INFO] DFAST_QC result json was written to GCA_003136435.1_20111000_E3D_genomic.fna/dqc_result.json
[2023-06-17 02:02:53,022] [INFO] DFAST_QC completed!
[2023-06-17 02:02:53,022] [INFO] Total running time: 0h0m60s