[2023-06-08 03:42:42,804] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:42,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:42,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa13c152-61ca-4c1d-bca7-159df8871c8c/dqc_reference
[2023-06-08 03:42:44,789] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:44,790] [INFO] Task started: Prodigal
[2023-06-08 03:42:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fcf811e-c950-4438-ab8e-c31ef2a0ad4d/GCA_902514775.1_AG-325-A22_genomic.fna.gz | prodigal -d GCA_902514775.1_AG-325-A22_genomic.fna/cds.fna -a GCA_902514775.1_AG-325-A22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:46,368] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:46,369] [INFO] Task started: HMMsearch
[2023-06-08 03:42:46,369] [INFO] Running command: hmmsearch --tblout GCA_902514775.1_AG-325-A22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa13c152-61ca-4c1d-bca7-159df8871c8c/dqc_reference/reference_markers.hmm GCA_902514775.1_AG-325-A22_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:46,578] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:46,580] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2fcf811e-c950-4438-ab8e-c31ef2a0ad4d/GCA_902514775.1_AG-325-A22_genomic.fna.gz]
[2023-06-08 03:42:46,601] [INFO] Query marker FASTA was written to GCA_902514775.1_AG-325-A22_genomic.fna/markers.fasta
[2023-06-08 03:42:46,601] [INFO] Task started: Blastn
[2023-06-08 03:42:46,602] [INFO] Running command: blastn -query GCA_902514775.1_AG-325-A22_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa13c152-61ca-4c1d-bca7-159df8871c8c/dqc_reference/reference_markers.fasta -out GCA_902514775.1_AG-325-A22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:47,396] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:47,400] [INFO] Selected 15 target genomes.
[2023-06-08 03:42:47,400] [INFO] Target genome list was writen to GCA_902514775.1_AG-325-A22_genomic.fna/target_genomes.txt
[2023-06-08 03:42:47,418] [INFO] Task started: fastANI
[2023-06-08 03:42:47,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fcf811e-c950-4438-ab8e-c31ef2a0ad4d/GCA_902514775.1_AG-325-A22_genomic.fna.gz --refList GCA_902514775.1_AG-325-A22_genomic.fna/target_genomes.txt --output GCA_902514775.1_AG-325-A22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:42:56,252] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:56,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa13c152-61ca-4c1d-bca7-159df8871c8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:42:56,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa13c152-61ca-4c1d-bca7-159df8871c8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:42:56,255] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:42:56,255] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:42:56,255] [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
--------------------------------------------------------------------------------
[2023-06-08 03:42:56,257] [INFO] DFAST Taxonomy check result was written to GCA_902514775.1_AG-325-A22_genomic.fna/tc_result.tsv
[2023-06-08 03:42:56,258] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:42:56,258] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:42:56,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa13c152-61ca-4c1d-bca7-159df8871c8c/dqc_reference/checkm_data
[2023-06-08 03:42:56,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:42:56,278] [INFO] Task started: CheckM
[2023-06-08 03:42:56,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902514775.1_AG-325-A22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902514775.1_AG-325-A22_genomic.fna/checkm_input GCA_902514775.1_AG-325-A22_genomic.fna/checkm_result
[2023-06-08 03:43:10,876] [INFO] Task succeeded: CheckM
[2023-06-08 03:43:10,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:43:10,912] [INFO] ===== Completeness check finished =====
[2023-06-08 03:43:10,912] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:43:10,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902514775.1_AG-325-A22_genomic.fna/markers.fasta)
[2023-06-08 03:43:10,913] [INFO] Task started: Blastn
[2023-06-08 03:43:10,913] [INFO] Running command: blastn -query GCA_902514775.1_AG-325-A22_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa13c152-61ca-4c1d-bca7-159df8871c8c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902514775.1_AG-325-A22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:43:11,819] [INFO] Task succeeded: Blastn
[2023-06-08 03:43:11,822] [INFO] Selected 9 target genomes.
[2023-06-08 03:43:11,822] [INFO] Target genome list was writen to GCA_902514775.1_AG-325-A22_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:43:11,827] [INFO] Task started: fastANI
[2023-06-08 03:43:11,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fcf811e-c950-4438-ab8e-c31ef2a0ad4d/GCA_902514775.1_AG-325-A22_genomic.fna.gz --refList GCA_902514775.1_AG-325-A22_genomic.fna/target_genomes_gtdb.txt --output GCA_902514775.1_AG-325-A22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:43:14,181] [INFO] Task succeeded: fastANI
[2023-06-08 03:43:14,196] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:43:14,197] [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_902606175.1	s__GCA-2707915 sp902606175	95.3335	203	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.24	95.17	0.72	0.71	3	conclusive
GCA_902542325.1	s__GCA-2707915 sp902542325	91.9408	192	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.62	99.62	0.80	0.80	2	-
GCA_902604855.1	s__GCA-2707915 sp902604855	91.2147	202	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574355.1	s__GCA-2707915 sp902574355	90.9157	219	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902605935.1	s__GCA-2707915 sp902605935	90.845	114	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618945.1	s__GCA-2707915 sp902618945	89.3236	204	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.64	95.64	0.79	0.79	2	-
GCA_902620785.1	s__GCA-2707915 sp902620785	89.114	222	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	-
GCA_902517565.1	s__GCA-2707915 sp902517565	78.9107	87	277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:43:14,199] [INFO] GTDB search result was written to GCA_902514775.1_AG-325-A22_genomic.fna/result_gtdb.tsv
[2023-06-08 03:43:14,199] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:43:14,203] [INFO] DFAST_QC result json was written to GCA_902514775.1_AG-325-A22_genomic.fna/dqc_result.json
[2023-06-08 03:43:14,204] [INFO] DFAST_QC completed!
[2023-06-08 03:43:14,204] [INFO] Total running time: 0h0m31s