[2023-06-29 12:09:43,506] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:09:43,518] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:09:43,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c92a1d8-5028-4b75-a781-c381b82851cf/dqc_reference
[2023-06-29 12:09:44,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:09:44,830] [INFO] Task started: Prodigal
[2023-06-29 12:09:44,830] [INFO] Running command: gunzip -c /var/lib/cwl/stgf27b6351-cd2a-4a17-a548-c9cf1ff7b07a/GCA_020352215.1_ASM2035221v1_genomic.fna.gz | prodigal -d GCA_020352215.1_ASM2035221v1_genomic.fna/cds.fna -a GCA_020352215.1_ASM2035221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:10:04,292] [INFO] Task succeeded: Prodigal
[2023-06-29 12:10:04,293] [INFO] Task started: HMMsearch
[2023-06-29 12:10:04,293] [INFO] Running command: hmmsearch --tblout GCA_020352215.1_ASM2035221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c92a1d8-5028-4b75-a781-c381b82851cf/dqc_reference/reference_markers.hmm GCA_020352215.1_ASM2035221v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:10:04,655] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:10:04,657] [INFO] Found 6/6 markers.
[2023-06-29 12:10:04,722] [INFO] Query marker FASTA was written to GCA_020352215.1_ASM2035221v1_genomic.fna/markers.fasta
[2023-06-29 12:10:04,723] [INFO] Task started: Blastn
[2023-06-29 12:10:04,723] [INFO] Running command: blastn -query GCA_020352215.1_ASM2035221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c92a1d8-5028-4b75-a781-c381b82851cf/dqc_reference/reference_markers.fasta -out GCA_020352215.1_ASM2035221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:10:05,338] [INFO] Task succeeded: Blastn
[2023-06-29 12:10:05,346] [INFO] Selected 24 target genomes.
[2023-06-29 12:10:05,346] [INFO] Target genome list was writen to GCA_020352215.1_ASM2035221v1_genomic.fna/target_genomes.txt
[2023-06-29 12:10:05,368] [INFO] Task started: fastANI
[2023-06-29 12:10:05,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27b6351-cd2a-4a17-a548-c9cf1ff7b07a/GCA_020352215.1_ASM2035221v1_genomic.fna.gz --refList GCA_020352215.1_ASM2035221v1_genomic.fna/target_genomes.txt --output GCA_020352215.1_ASM2035221v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:10:23,829] [INFO] Task succeeded: fastANI
[2023-06-29 12:10:23,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c92a1d8-5028-4b75-a781-c381b82851cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:10:23,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c92a1d8-5028-4b75-a781-c381b82851cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:10:23,832] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:10:23,832] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:10:23,832] [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
--------------------------------------------------------------------------------
[2023-06-29 12:10:23,834] [INFO] DFAST Taxonomy check result was written to GCA_020352215.1_ASM2035221v1_genomic.fna/tc_result.tsv
[2023-06-29 12:10:23,835] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:10:23,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:10:23,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c92a1d8-5028-4b75-a781-c381b82851cf/dqc_reference/checkm_data
[2023-06-29 12:10:23,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:10:23,899] [INFO] Task started: CheckM
[2023-06-29 12:10:23,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020352215.1_ASM2035221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020352215.1_ASM2035221v1_genomic.fna/checkm_input GCA_020352215.1_ASM2035221v1_genomic.fna/checkm_result
[2023-06-29 12:11:18,926] [INFO] Task succeeded: CheckM
[2023-06-29 12:11:18,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:11:18,954] [INFO] ===== Completeness check finished =====
[2023-06-29 12:11:18,954] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:11:18,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020352215.1_ASM2035221v1_genomic.fna/markers.fasta)
[2023-06-29 12:11:18,955] [INFO] Task started: Blastn
[2023-06-29 12:11:18,955] [INFO] Running command: blastn -query GCA_020352215.1_ASM2035221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c92a1d8-5028-4b75-a781-c381b82851cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_020352215.1_ASM2035221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:11:19,781] [INFO] Task succeeded: Blastn
[2023-06-29 12:11:19,790] [INFO] Selected 24 target genomes.
[2023-06-29 12:11:19,791] [INFO] Target genome list was writen to GCA_020352215.1_ASM2035221v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:11:19,823] [INFO] Task started: fastANI
[2023-06-29 12:11:19,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27b6351-cd2a-4a17-a548-c9cf1ff7b07a/GCA_020352215.1_ASM2035221v1_genomic.fna.gz --refList GCA_020352215.1_ASM2035221v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020352215.1_ASM2035221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:11:37,576] [INFO] Task succeeded: fastANI
[2023-06-29 12:11:37,591] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:11:37,591] [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_016782865.1	s__SG8-4 sp016782865	76.3964	178	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__SG8-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001303465.1	s__SG8-4 sp001303465	76.3536	110	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__SG8-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934255.1	s__JAFGPJ01 sp016934255	75.7908	95	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__JAFGPJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603075.1	s__PLanc-01 sp001603075	75.7115	109	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013202635.1	s__NIOZ-UU13 sp013202635	75.6974	67	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__NIOZ-UU13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932835.1	s__JAFGCD01 sp016932835	75.6852	67	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__JAFGCD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933985.1	s__JAFGCD01 sp016933985	75.6027	88	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__JAFGCD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932895.1	s__PLanc-01 sp016932895	75.5612	143	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327785.1	s__PLanc-01 sp002327785	75.502	104	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928975.1	s__PLanc-01 sp016928975	75.4953	109	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055905.1	s__PLanc-01 sp018055905	75.3838	57	2066	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:11:37,593] [INFO] GTDB search result was written to GCA_020352215.1_ASM2035221v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:11:37,594] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:11:37,602] [INFO] DFAST_QC result json was written to GCA_020352215.1_ASM2035221v1_genomic.fna/dqc_result.json
[2023-06-29 12:11:37,602] [INFO] DFAST_QC completed!
[2023-06-29 12:11:37,603] [INFO] Total running time: 0h1m54s