[2023-06-28 09:15:06,961] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:15:06,971] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:15:06,972] [INFO] DQC Reference Directory: /var/lib/cwl/stga385860e-652b-42af-8551-f36d49df3ff1/dqc_reference
[2023-06-28 09:15:09,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:15:09,272] [INFO] Task started: Prodigal
[2023-06-28 09:15:09,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg514d0316-9c31-4877-a5b3-4e8e461510da/GCA_017628415.1_ASM1762841v1_genomic.fna.gz | prodigal -d GCA_017628415.1_ASM1762841v1_genomic.fna/cds.fna -a GCA_017628415.1_ASM1762841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:15:21,209] [INFO] Task succeeded: Prodigal
[2023-06-28 09:15:21,210] [INFO] Task started: HMMsearch
[2023-06-28 09:15:21,210] [INFO] Running command: hmmsearch --tblout GCA_017628415.1_ASM1762841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga385860e-652b-42af-8551-f36d49df3ff1/dqc_reference/reference_markers.hmm GCA_017628415.1_ASM1762841v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:15:21,414] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:15:21,416] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg514d0316-9c31-4877-a5b3-4e8e461510da/GCA_017628415.1_ASM1762841v1_genomic.fna.gz]
[2023-06-28 09:15:21,442] [INFO] Query marker FASTA was written to GCA_017628415.1_ASM1762841v1_genomic.fna/markers.fasta
[2023-06-28 09:15:21,442] [INFO] Task started: Blastn
[2023-06-28 09:15:21,442] [INFO] Running command: blastn -query GCA_017628415.1_ASM1762841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga385860e-652b-42af-8551-f36d49df3ff1/dqc_reference/reference_markers.fasta -out GCA_017628415.1_ASM1762841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:15:22,010] [INFO] Task succeeded: Blastn
[2023-06-28 09:15:22,014] [INFO] Selected 25 target genomes.
[2023-06-28 09:15:22,015] [INFO] Target genome list was writen to GCA_017628415.1_ASM1762841v1_genomic.fna/target_genomes.txt
[2023-06-28 09:15:22,019] [INFO] Task started: fastANI
[2023-06-28 09:15:22,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg514d0316-9c31-4877-a5b3-4e8e461510da/GCA_017628415.1_ASM1762841v1_genomic.fna.gz --refList GCA_017628415.1_ASM1762841v1_genomic.fna/target_genomes.txt --output GCA_017628415.1_ASM1762841v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:15:33,975] [INFO] Task succeeded: fastANI
[2023-06-28 09:15:33,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga385860e-652b-42af-8551-f36d49df3ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:15:33,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga385860e-652b-42af-8551-f36d49df3ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:15:33,978] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:15:33,978] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 09:15:33,979] [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 09:15:33,981] [INFO] DFAST Taxonomy check result was written to GCA_017628415.1_ASM1762841v1_genomic.fna/tc_result.tsv
[2023-06-28 09:15:33,982] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:15:33,982] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:15:33,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga385860e-652b-42af-8551-f36d49df3ff1/dqc_reference/checkm_data
[2023-06-28 09:15:33,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:15:34,015] [INFO] Task started: CheckM
[2023-06-28 09:15:34,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017628415.1_ASM1762841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017628415.1_ASM1762841v1_genomic.fna/checkm_input GCA_017628415.1_ASM1762841v1_genomic.fna/checkm_result
[2023-06-28 09:16:11,621] [INFO] Task succeeded: CheckM
[2023-06-28 09:16:11,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.25%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 09:16:11,644] [INFO] ===== Completeness check finished =====
[2023-06-28 09:16:11,644] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:16:11,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017628415.1_ASM1762841v1_genomic.fna/markers.fasta)
[2023-06-28 09:16:11,645] [INFO] Task started: Blastn
[2023-06-28 09:16:11,645] [INFO] Running command: blastn -query GCA_017628415.1_ASM1762841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga385860e-652b-42af-8551-f36d49df3ff1/dqc_reference/reference_markers_gtdb.fasta -out GCA_017628415.1_ASM1762841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:16:12,196] [INFO] Task succeeded: Blastn
[2023-06-28 09:16:12,201] [INFO] Selected 14 target genomes.
[2023-06-28 09:16:12,201] [INFO] Target genome list was writen to GCA_017628415.1_ASM1762841v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:16:12,212] [INFO] Task started: fastANI
[2023-06-28 09:16:12,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg514d0316-9c31-4877-a5b3-4e8e461510da/GCA_017628415.1_ASM1762841v1_genomic.fna.gz --refList GCA_017628415.1_ASM1762841v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017628415.1_ASM1762841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:16:18,743] [INFO] Task succeeded: fastANI
[2023-06-28 09:16:18,762] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 09:16:18,763] [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_017424485.1	s__UBA1189 sp017424485	81.9478	266	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557005.1	s__UBA1189 sp017557005	80.7042	319	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	97.00	97.00	0.79	0.79	2	-
GCA_017622495.1	s__UBA1189 sp017622495	80.5565	305	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	97.35	97.10	0.83	0.80	5	-
GCA_015060865.1	s__UBA1189 sp015060865	80.5518	294	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465905.1	s__UBA1189 sp017465905	80.3701	295	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017517925.1	s__UBA1189 sp017517925	80.0679	234	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556045.1	s__UBA1189 sp017556045	79.9496	247	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555875.1	s__UBA1189 sp017555875	79.8147	227	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548225.1	s__UBA1189 sp017548225	79.3779	167	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017520935.1	s__UBA1189 sp017520935	79.1177	284	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	97.28	97.28	0.79	0.79	2	-
GCA_017517605.1	s__Phocaeicola_A sp017517605	76.6946	52	647	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.50	97.50	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-06-28 09:16:18,765] [INFO] GTDB search result was written to GCA_017628415.1_ASM1762841v1_genomic.fna/result_gtdb.tsv
[2023-06-28 09:16:18,766] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:16:18,769] [INFO] DFAST_QC result json was written to GCA_017628415.1_ASM1762841v1_genomic.fna/dqc_result.json
[2023-06-28 09:16:18,769] [INFO] DFAST_QC completed!
[2023-06-28 09:16:18,770] [INFO] Total running time: 0h1m12s