[2023-06-19 05:51:05,357] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:05,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:05,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b32199e-c80e-44c3-8ba9-41786ff90824/dqc_reference
[2023-06-19 05:51:07,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:51:07,620] [INFO] Task started: Prodigal
[2023-06-19 05:51:07,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg960175d3-be71-43f3-97ed-b39eb7160d16/GCA_014847185.1_ASM1484718v1_genomic.fna.gz | prodigal -d GCA_014847185.1_ASM1484718v1_genomic.fna/cds.fna -a GCA_014847185.1_ASM1484718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:51:11,394] [INFO] Task succeeded: Prodigal
[2023-06-19 05:51:11,395] [INFO] Task started: HMMsearch
[2023-06-19 05:51:11,395] [INFO] Running command: hmmsearch --tblout GCA_014847185.1_ASM1484718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b32199e-c80e-44c3-8ba9-41786ff90824/dqc_reference/reference_markers.hmm GCA_014847185.1_ASM1484718v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:51:11,611] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:51:11,613] [INFO] Found 6/6 markers.
[2023-06-19 05:51:11,647] [INFO] Query marker FASTA was written to GCA_014847185.1_ASM1484718v1_genomic.fna/markers.fasta
[2023-06-19 05:51:11,648] [INFO] Task started: Blastn
[2023-06-19 05:51:11,648] [INFO] Running command: blastn -query GCA_014847185.1_ASM1484718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b32199e-c80e-44c3-8ba9-41786ff90824/dqc_reference/reference_markers.fasta -out GCA_014847185.1_ASM1484718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:51:12,886] [INFO] Task succeeded: Blastn
[2023-06-19 05:51:12,892] [INFO] Selected 22 target genomes.
[2023-06-19 05:51:12,893] [INFO] Target genome list was writen to GCA_014847185.1_ASM1484718v1_genomic.fna/target_genomes.txt
[2023-06-19 05:51:12,903] [INFO] Task started: fastANI
[2023-06-19 05:51:12,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg960175d3-be71-43f3-97ed-b39eb7160d16/GCA_014847185.1_ASM1484718v1_genomic.fna.gz --refList GCA_014847185.1_ASM1484718v1_genomic.fna/target_genomes.txt --output GCA_014847185.1_ASM1484718v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:51:21,828] [INFO] Task succeeded: fastANI
[2023-06-19 05:51:21,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b32199e-c80e-44c3-8ba9-41786ff90824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:51:21,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b32199e-c80e-44c3-8ba9-41786ff90824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:51:21,832] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:51:21,832] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:51:21,832] [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
--------------------------------------------------------------------------------
[2023-06-19 05:51:21,835] [INFO] DFAST Taxonomy check result was written to GCA_014847185.1_ASM1484718v1_genomic.fna/tc_result.tsv
[2023-06-19 05:51:21,836] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:51:21,836] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:51:21,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b32199e-c80e-44c3-8ba9-41786ff90824/dqc_reference/checkm_data
[2023-06-19 05:51:21,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:51:21,865] [INFO] Task started: CheckM
[2023-06-19 05:51:21,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014847185.1_ASM1484718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014847185.1_ASM1484718v1_genomic.fna/checkm_input GCA_014847185.1_ASM1484718v1_genomic.fna/checkm_result
[2023-06-19 05:51:40,903] [INFO] Task succeeded: CheckM
[2023-06-19 05:51:40,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:51:40,935] [INFO] ===== Completeness check finished =====
[2023-06-19 05:51:40,935] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:51:40,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014847185.1_ASM1484718v1_genomic.fna/markers.fasta)
[2023-06-19 05:51:40,936] [INFO] Task started: Blastn
[2023-06-19 05:51:40,937] [INFO] Running command: blastn -query GCA_014847185.1_ASM1484718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b32199e-c80e-44c3-8ba9-41786ff90824/dqc_reference/reference_markers_gtdb.fasta -out GCA_014847185.1_ASM1484718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:51:41,824] [INFO] Task succeeded: Blastn
[2023-06-19 05:51:41,830] [INFO] Selected 11 target genomes.
[2023-06-19 05:51:41,831] [INFO] Target genome list was writen to GCA_014847185.1_ASM1484718v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:51:41,838] [INFO] Task started: fastANI
[2023-06-19 05:51:41,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg960175d3-be71-43f3-97ed-b39eb7160d16/GCA_014847185.1_ASM1484718v1_genomic.fna.gz --refList GCA_014847185.1_ASM1484718v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014847185.1_ASM1484718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:51:46,440] [INFO] Task succeeded: fastANI
[2023-06-19 05:51:46,453] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:51:46,453] [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_002102825.1	s__Zag111 sp002102825	98.829	523	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.43	98.83	0.94	0.90	9	conclusive
GCA_002438405.1	s__Zag111 sp002438405	90.7556	533	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.96	99.93	0.99	0.98	3	-
GCA_002103105.1	s__Zag111 sp002103105	80.6172	362	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	97.50	95.26	0.92	0.84	7	-
GCA_905215335.1	s__Zag111 sp905215335	79.8033	333	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258735.1	s__Zag111 sp003258735	79.6668	321	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.31	98.12	0.91	0.82	5	-
GCA_002405805.1	s__Zag111 sp002405805	79.6158	303	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803505.1	s__Zag111 sp014803505	79.3143	290	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555325.1	s__Zag111 sp900555325	79.2247	235	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.12	99.12	0.81	0.81	2	-
GCA_905211505.1	s__Zag111 sp905211505	79.11	143	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536545.1	s__Zag111 sp017536545	78.9499	267	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626055.1	s__Zag111 sp017626055	78.8873	275	629	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 05:51:46,455] [INFO] GTDB search result was written to GCA_014847185.1_ASM1484718v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:51:46,455] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:51:46,459] [INFO] DFAST_QC result json was written to GCA_014847185.1_ASM1484718v1_genomic.fna/dqc_result.json
[2023-06-19 05:51:46,459] [INFO] DFAST_QC completed!
[2023-06-19 05:51:46,460] [INFO] Total running time: 0h0m41s