[2023-06-28 18:28:03,146] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:28:03,150] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:28:03,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg0566ff2c-fa5b-426e-9b57-98921e0b34a3/dqc_reference
[2023-06-28 18:28:05,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:28:05,451] [INFO] Task started: Prodigal
[2023-06-28 18:28:05,452] [INFO] Running command: gunzip -c /var/lib/cwl/stg15fd62b1-cb09-465d-8fa1-2565f0f22faf/GCA_017536545.1_ASM1753654v1_genomic.fna.gz | prodigal -d GCA_017536545.1_ASM1753654v1_genomic.fna/cds.fna -a GCA_017536545.1_ASM1753654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:28:08,980] [INFO] Task succeeded: Prodigal
[2023-06-28 18:28:08,980] [INFO] Task started: HMMsearch
[2023-06-28 18:28:08,980] [INFO] Running command: hmmsearch --tblout GCA_017536545.1_ASM1753654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0566ff2c-fa5b-426e-9b57-98921e0b34a3/dqc_reference/reference_markers.hmm GCA_017536545.1_ASM1753654v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:28:09,214] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:28:09,216] [INFO] Found 6/6 markers.
[2023-06-28 18:28:09,241] [INFO] Query marker FASTA was written to GCA_017536545.1_ASM1753654v1_genomic.fna/markers.fasta
[2023-06-28 18:28:09,242] [INFO] Task started: Blastn
[2023-06-28 18:28:09,242] [INFO] Running command: blastn -query GCA_017536545.1_ASM1753654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0566ff2c-fa5b-426e-9b57-98921e0b34a3/dqc_reference/reference_markers.fasta -out GCA_017536545.1_ASM1753654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:28:09,824] [INFO] Task succeeded: Blastn
[2023-06-28 18:28:09,828] [INFO] Selected 20 target genomes.
[2023-06-28 18:28:09,829] [INFO] Target genome list was writen to GCA_017536545.1_ASM1753654v1_genomic.fna/target_genomes.txt
[2023-06-28 18:28:09,861] [INFO] Task started: fastANI
[2023-06-28 18:28:09,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg15fd62b1-cb09-465d-8fa1-2565f0f22faf/GCA_017536545.1_ASM1753654v1_genomic.fna.gz --refList GCA_017536545.1_ASM1753654v1_genomic.fna/target_genomes.txt --output GCA_017536545.1_ASM1753654v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:28:18,705] [INFO] Task succeeded: fastANI
[2023-06-28 18:28:18,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0566ff2c-fa5b-426e-9b57-98921e0b34a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:28:18,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0566ff2c-fa5b-426e-9b57-98921e0b34a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:28:18,708] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:28:18,708] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:28:18,708] [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 18:28:18,711] [INFO] DFAST Taxonomy check result was written to GCA_017536545.1_ASM1753654v1_genomic.fna/tc_result.tsv
[2023-06-28 18:28:18,711] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:28:18,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:28:18,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0566ff2c-fa5b-426e-9b57-98921e0b34a3/dqc_reference/checkm_data
[2023-06-28 18:28:18,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:28:18,740] [INFO] Task started: CheckM
[2023-06-28 18:28:18,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017536545.1_ASM1753654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017536545.1_ASM1753654v1_genomic.fna/checkm_input GCA_017536545.1_ASM1753654v1_genomic.fna/checkm_result
[2023-06-28 18:28:36,980] [INFO] Task succeeded: CheckM
[2023-06-28 18:28:36,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:28:37,002] [INFO] ===== Completeness check finished =====
[2023-06-28 18:28:37,002] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:28:37,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017536545.1_ASM1753654v1_genomic.fna/markers.fasta)
[2023-06-28 18:28:37,003] [INFO] Task started: Blastn
[2023-06-28 18:28:37,003] [INFO] Running command: blastn -query GCA_017536545.1_ASM1753654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0566ff2c-fa5b-426e-9b57-98921e0b34a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_017536545.1_ASM1753654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:28:37,839] [INFO] Task succeeded: Blastn
[2023-06-28 18:28:37,844] [INFO] Selected 10 target genomes.
[2023-06-28 18:28:37,844] [INFO] Target genome list was writen to GCA_017536545.1_ASM1753654v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:28:37,921] [INFO] Task started: fastANI
[2023-06-28 18:28:37,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg15fd62b1-cb09-465d-8fa1-2565f0f22faf/GCA_017536545.1_ASM1753654v1_genomic.fna.gz --refList GCA_017536545.1_ASM1753654v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017536545.1_ASM1753654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:28:42,351] [INFO] Task succeeded: fastANI
[2023-06-28 18:28:42,371] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:28:42,371] [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_017536545.1	s__Zag111 sp017536545	100.0	614	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017626055.1	s__Zag111 sp017626055	89.0726	516	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472545.1	s__Zag111 sp017472545	84.5078	341	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215335.1	s__Zag111 sp905215335	79.5847	324	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015152555.1	s__Zag111 sp015152555	79.3794	285	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002103105.1	s__Zag111 sp002103105	79.3023	290	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	97.50	95.26	0.92	0.84	7	-
GCA_003258735.1	s__Zag111 sp003258735	79.0222	294	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.31	98.12	0.91	0.82	5	-
GCA_002438405.1	s__Zag111 sp002438405	78.9665	299	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.96	99.93	0.99	0.98	3	-
GCA_002405805.1	s__Zag111 sp002405805	78.8693	282	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017467605.1	s__Zag111 sp017467605	78.1782	248	620	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:28:42,374] [INFO] GTDB search result was written to GCA_017536545.1_ASM1753654v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:28:42,375] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:28:42,379] [INFO] DFAST_QC result json was written to GCA_017536545.1_ASM1753654v1_genomic.fna/dqc_result.json
[2023-06-28 18:28:42,379] [INFO] DFAST_QC completed!
[2023-06-28 18:28:42,380] [INFO] Total running time: 0h0m39s