[2023-06-28 12:34:08,388] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:34:08,393] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:34:08,393] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1970059-0c11-428c-acdb-287656ae1711/dqc_reference
[2023-06-28 12:34:09,960] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:34:09,961] [INFO] Task started: Prodigal
[2023-06-28 12:34:09,961] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3a7c690-4cfe-4fc1-a6c5-f51e98c2e8dc/GCA_017995595.1_ASM1799559v1_genomic.fna.gz | prodigal -d GCA_017995595.1_ASM1799559v1_genomic.fna/cds.fna -a GCA_017995595.1_ASM1799559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:34:12,195] [INFO] Task succeeded: Prodigal
[2023-06-28 12:34:12,196] [INFO] Task started: HMMsearch
[2023-06-28 12:34:12,196] [INFO] Running command: hmmsearch --tblout GCA_017995595.1_ASM1799559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1970059-0c11-428c-acdb-287656ae1711/dqc_reference/reference_markers.hmm GCA_017995595.1_ASM1799559v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:34:12,398] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:34:12,400] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb3a7c690-4cfe-4fc1-a6c5-f51e98c2e8dc/GCA_017995595.1_ASM1799559v1_genomic.fna.gz]
[2023-06-28 12:34:12,426] [INFO] Query marker FASTA was written to GCA_017995595.1_ASM1799559v1_genomic.fna/markers.fasta
[2023-06-28 12:34:12,427] [INFO] Task started: Blastn
[2023-06-28 12:34:12,427] [INFO] Running command: blastn -query GCA_017995595.1_ASM1799559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1970059-0c11-428c-acdb-287656ae1711/dqc_reference/reference_markers.fasta -out GCA_017995595.1_ASM1799559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:13,003] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:13,007] [INFO] Selected 20 target genomes.
[2023-06-28 12:34:13,007] [INFO] Target genome list was writen to GCA_017995595.1_ASM1799559v1_genomic.fna/target_genomes.txt
[2023-06-28 12:34:13,009] [INFO] Task started: fastANI
[2023-06-28 12:34:13,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a7c690-4cfe-4fc1-a6c5-f51e98c2e8dc/GCA_017995595.1_ASM1799559v1_genomic.fna.gz --refList GCA_017995595.1_ASM1799559v1_genomic.fna/target_genomes.txt --output GCA_017995595.1_ASM1799559v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:34:21,499] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:21,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1970059-0c11-428c-acdb-287656ae1711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:34:21,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1970059-0c11-428c-acdb-287656ae1711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:34:21,501] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:34:21,501] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:34:21,501] [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 12:34:21,503] [INFO] DFAST Taxonomy check result was written to GCA_017995595.1_ASM1799559v1_genomic.fna/tc_result.tsv
[2023-06-28 12:34:21,504] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:34:21,504] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:34:21,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1970059-0c11-428c-acdb-287656ae1711/dqc_reference/checkm_data
[2023-06-28 12:34:21,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:34:21,529] [INFO] Task started: CheckM
[2023-06-28 12:34:21,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017995595.1_ASM1799559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017995595.1_ASM1799559v1_genomic.fna/checkm_input GCA_017995595.1_ASM1799559v1_genomic.fna/checkm_result
[2023-06-28 12:34:37,366] [INFO] Task succeeded: CheckM
[2023-06-28 12:34:37,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:34:37,389] [INFO] ===== Completeness check finished =====
[2023-06-28 12:34:37,390] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:34:37,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017995595.1_ASM1799559v1_genomic.fna/markers.fasta)
[2023-06-28 12:34:37,391] [INFO] Task started: Blastn
[2023-06-28 12:34:37,391] [INFO] Running command: blastn -query GCA_017995595.1_ASM1799559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1970059-0c11-428c-acdb-287656ae1711/dqc_reference/reference_markers_gtdb.fasta -out GCA_017995595.1_ASM1799559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:38,182] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:38,187] [INFO] Selected 19 target genomes.
[2023-06-28 12:34:38,187] [INFO] Target genome list was writen to GCA_017995595.1_ASM1799559v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:34:38,191] [INFO] Task started: fastANI
[2023-06-28 12:34:38,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a7c690-4cfe-4fc1-a6c5-f51e98c2e8dc/GCA_017995595.1_ASM1799559v1_genomic.fna.gz --refList GCA_017995595.1_ASM1799559v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017995595.1_ASM1799559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:34:43,942] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:43,954] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:34:43,954] [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_017995595.1	s__JAGOIO01 sp017995595	100.0	336	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__JAGOIO01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000437435.1	s__Stercorousia sp000437435	77.1512	53	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.52	97.52	0.91	0.91	3	-
GCA_003258725.1	s__UBA6984 sp003258725	77.1507	53	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	98.56	98.53	0.92	0.92	3	-
GCA_905212085.1	s__Stercorousia sp905212085	76.9999	56	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015152455.1	s__SIG32 sp015152455	76.8912	58	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__SIG32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550295.1	s__UBA6984 sp900550295	76.8112	51	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	99.30	99.12	0.94	0.93	3	-
GCA_002102825.1	s__Zag111 sp002102825	76.7926	50	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.43	98.83	0.94	0.90	9	-
GCA_905215335.1	s__Zag111 sp905215335	76.6788	51	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803265.1	s__UBA791 sp902803265	76.6373	51	341	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:34:43,957] [INFO] GTDB search result was written to GCA_017995595.1_ASM1799559v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:34:43,957] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:34:43,960] [INFO] DFAST_QC result json was written to GCA_017995595.1_ASM1799559v1_genomic.fna/dqc_result.json
[2023-06-28 12:34:43,961] [INFO] DFAST_QC completed!
[2023-06-28 12:34:43,961] [INFO] Total running time: 0h0m36s