[2023-06-28 14:39:01,799] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:39:01,822] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:39:01,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg0443a4e1-9d86-496d-b358-91f56782b23b/dqc_reference
[2023-06-28 14:39:04,107] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:39:04,111] [INFO] Task started: Prodigal
[2023-06-28 14:39:04,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg0be81dd4-553a-454a-a9b6-a71d1e0fad24/GCA_005223045.1_ASM522304v1_genomic.fna.gz | prodigal -d GCA_005223045.1_ASM522304v1_genomic.fna/cds.fna -a GCA_005223045.1_ASM522304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:39:20,872] [INFO] Task succeeded: Prodigal
[2023-06-28 14:39:20,873] [INFO] Task started: HMMsearch
[2023-06-28 14:39:20,873] [INFO] Running command: hmmsearch --tblout GCA_005223045.1_ASM522304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0443a4e1-9d86-496d-b358-91f56782b23b/dqc_reference/reference_markers.hmm GCA_005223045.1_ASM522304v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:39:21,253] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:39:21,255] [INFO] Found 6/6 markers.
[2023-06-28 14:39:21,307] [INFO] Query marker FASTA was written to GCA_005223045.1_ASM522304v1_genomic.fna/markers.fasta
[2023-06-28 14:39:21,308] [INFO] Task started: Blastn
[2023-06-28 14:39:21,308] [INFO] Running command: blastn -query GCA_005223045.1_ASM522304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0443a4e1-9d86-496d-b358-91f56782b23b/dqc_reference/reference_markers.fasta -out GCA_005223045.1_ASM522304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:39:21,992] [INFO] Task succeeded: Blastn
[2023-06-28 14:39:21,996] [INFO] Selected 14 target genomes.
[2023-06-28 14:39:21,997] [INFO] Target genome list was writen to GCA_005223045.1_ASM522304v1_genomic.fna/target_genomes.txt
[2023-06-28 14:39:22,017] [INFO] Task started: fastANI
[2023-06-28 14:39:22,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg0be81dd4-553a-454a-a9b6-a71d1e0fad24/GCA_005223045.1_ASM522304v1_genomic.fna.gz --refList GCA_005223045.1_ASM522304v1_genomic.fna/target_genomes.txt --output GCA_005223045.1_ASM522304v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:39:28,439] [INFO] Task succeeded: fastANI
[2023-06-28 14:39:28,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0443a4e1-9d86-496d-b358-91f56782b23b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:39:28,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0443a4e1-9d86-496d-b358-91f56782b23b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:39:28,442] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:39:28,442] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:39:28,442] [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
--------------------------------------------------------------------------------
[2023-06-28 14:39:28,445] [INFO] DFAST Taxonomy check result was written to GCA_005223045.1_ASM522304v1_genomic.fna/tc_result.tsv
[2023-06-28 14:39:28,446] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:39:28,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:39:28,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0443a4e1-9d86-496d-b358-91f56782b23b/dqc_reference/checkm_data
[2023-06-28 14:39:28,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:39:28,514] [INFO] Task started: CheckM
[2023-06-28 14:39:28,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005223045.1_ASM522304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005223045.1_ASM522304v1_genomic.fna/checkm_input GCA_005223045.1_ASM522304v1_genomic.fna/checkm_result
[2023-06-28 14:40:18,617] [INFO] Task succeeded: CheckM
[2023-06-28 14:40:18,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:40:18,645] [INFO] ===== Completeness check finished =====
[2023-06-28 14:40:18,645] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:40:18,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005223045.1_ASM522304v1_genomic.fna/markers.fasta)
[2023-06-28 14:40:18,646] [INFO] Task started: Blastn
[2023-06-28 14:40:18,646] [INFO] Running command: blastn -query GCA_005223045.1_ASM522304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0443a4e1-9d86-496d-b358-91f56782b23b/dqc_reference/reference_markers_gtdb.fasta -out GCA_005223045.1_ASM522304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:40:19,440] [INFO] Task succeeded: Blastn
[2023-06-28 14:40:19,445] [INFO] Selected 11 target genomes.
[2023-06-28 14:40:19,445] [INFO] Target genome list was writen to GCA_005223045.1_ASM522304v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:40:19,452] [INFO] Task started: fastANI
[2023-06-28 14:40:19,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg0be81dd4-553a-454a-a9b6-a71d1e0fad24/GCA_005223045.1_ASM522304v1_genomic.fna.gz --refList GCA_005223045.1_ASM522304v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005223045.1_ASM522304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:40:30,924] [INFO] Task succeeded: fastANI
[2023-06-28 14:40:30,944] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:40:30,945] [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_005223045.1	s__SG8-4 sp005223045	100.0	1968	1972	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	conclusive
GCA_016782865.1	s__SG8-4 sp016782865	79.8382	860	1972	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	78.5953	491	1972	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_014384025.1	s__NIOZ-UU13 sp014384025	76.9498	354	1972	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__NIOZ-UU13	95.0	99.70	99.70	0.88	0.88	2	-
GCA_016936275.1	s__JAFGPJ01 sp016936275	76.875	246	1972	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_013202635.1	s__NIOZ-UU13 sp013202635	76.6564	207	1972	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_016934255.1	s__JAFGPJ01 sp016934255	76.3455	260	1972	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_016932835.1	s__JAFGCD01 sp016932835	76.1392	88	1972	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_012517265.1	s__PLanc-01 sp012517265	75.9781	67	1972	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_017885385.1	s__JAFNGF01 sp017885385	75.7196	106	1972	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__JAFNGF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933295.1	s__JAFGPS01 sp016933295	75.7063	110	1972	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__JAFGPS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:40:31,071] [INFO] GTDB search result was written to GCA_005223045.1_ASM522304v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:40:31,072] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:40:31,076] [INFO] DFAST_QC result json was written to GCA_005223045.1_ASM522304v1_genomic.fna/dqc_result.json
[2023-06-28 14:40:31,076] [INFO] DFAST_QC completed!
[2023-06-28 14:40:31,077] [INFO] Total running time: 0h1m29s