[2023-06-30 10:58:45,539] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:58:45,541] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:58:45,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cb4a188-b72b-40f0-8aca-48d3a9c0bf35/dqc_reference
[2023-06-30 10:58:46,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:58:46,646] [INFO] Task started: Prodigal
[2023-06-30 10:58:46,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg571bbfe0-2c34-4ee1-b8ac-1e756d2e43b9/GCA_016200255.1_ASM1620025v1_genomic.fna.gz | prodigal -d GCA_016200255.1_ASM1620025v1_genomic.fna/cds.fna -a GCA_016200255.1_ASM1620025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:58:51,655] [INFO] Task succeeded: Prodigal
[2023-06-30 10:58:51,656] [INFO] Task started: HMMsearch
[2023-06-30 10:58:51,656] [INFO] Running command: hmmsearch --tblout GCA_016200255.1_ASM1620025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cb4a188-b72b-40f0-8aca-48d3a9c0bf35/dqc_reference/reference_markers.hmm GCA_016200255.1_ASM1620025v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:58:51,812] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:58:51,813] [INFO] Found 6/6 markers.
[2023-06-30 10:58:51,835] [INFO] Query marker FASTA was written to GCA_016200255.1_ASM1620025v1_genomic.fna/markers.fasta
[2023-06-30 10:58:51,835] [INFO] Task started: Blastn
[2023-06-30 10:58:51,835] [INFO] Running command: blastn -query GCA_016200255.1_ASM1620025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cb4a188-b72b-40f0-8aca-48d3a9c0bf35/dqc_reference/reference_markers.fasta -out GCA_016200255.1_ASM1620025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:58:52,402] [INFO] Task succeeded: Blastn
[2023-06-30 10:58:52,405] [INFO] Selected 15 target genomes.
[2023-06-30 10:58:52,405] [INFO] Target genome list was writen to GCA_016200255.1_ASM1620025v1_genomic.fna/target_genomes.txt
[2023-06-30 10:58:52,406] [INFO] Task started: fastANI
[2023-06-30 10:58:52,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg571bbfe0-2c34-4ee1-b8ac-1e756d2e43b9/GCA_016200255.1_ASM1620025v1_genomic.fna.gz --refList GCA_016200255.1_ASM1620025v1_genomic.fna/target_genomes.txt --output GCA_016200255.1_ASM1620025v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:59:04,528] [INFO] Task succeeded: fastANI
[2023-06-30 10:59:04,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cb4a188-b72b-40f0-8aca-48d3a9c0bf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:59:04,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cb4a188-b72b-40f0-8aca-48d3a9c0bf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:59:04,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:59:04,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:59:04,530] [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
--------------------------------------------------------------------------------
[2023-06-30 10:59:04,532] [INFO] DFAST Taxonomy check result was written to GCA_016200255.1_ASM1620025v1_genomic.fna/tc_result.tsv
[2023-06-30 10:59:04,532] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:59:04,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:59:04,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cb4a188-b72b-40f0-8aca-48d3a9c0bf35/dqc_reference/checkm_data
[2023-06-30 10:59:04,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:59:04,560] [INFO] Task started: CheckM
[2023-06-30 10:59:04,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016200255.1_ASM1620025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016200255.1_ASM1620025v1_genomic.fna/checkm_input GCA_016200255.1_ASM1620025v1_genomic.fna/checkm_result
[2023-06-30 10:59:24,235] [INFO] Task succeeded: CheckM
[2023-06-30 10:59:24,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 4.92%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 10:59:24,253] [INFO] ===== Completeness check finished =====
[2023-06-30 10:59:24,254] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:59:24,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016200255.1_ASM1620025v1_genomic.fna/markers.fasta)
[2023-06-30 10:59:24,254] [INFO] Task started: Blastn
[2023-06-30 10:59:24,254] [INFO] Running command: blastn -query GCA_016200255.1_ASM1620025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cb4a188-b72b-40f0-8aca-48d3a9c0bf35/dqc_reference/reference_markers_gtdb.fasta -out GCA_016200255.1_ASM1620025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:59:25,123] [INFO] Task succeeded: Blastn
[2023-06-30 10:59:25,126] [INFO] Selected 15 target genomes.
[2023-06-30 10:59:25,126] [INFO] Target genome list was writen to GCA_016200255.1_ASM1620025v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:59:25,142] [INFO] Task started: fastANI
[2023-06-30 10:59:25,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg571bbfe0-2c34-4ee1-b8ac-1e756d2e43b9/GCA_016200255.1_ASM1620025v1_genomic.fna.gz --refList GCA_016200255.1_ASM1620025v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016200255.1_ASM1620025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:59:32,057] [INFO] Task succeeded: fastANI
[2023-06-30 10:59:32,061] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:59:32,062] [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_016200255.1	s__JACQFA01 sp016200255	100.0	693	700	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__JACQBZ01;f__JACQBZ01;g__JACQFA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016201865.1	s__JACQCA01 sp016201865	81.6538	386	700	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__JACQBZ01;f__JACQBZ01;g__JACQCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016198945.1	s__JACQFA01 sp016198945	81.4622	272	700	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__JACQBZ01;f__JACQBZ01;g__JACQFA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016194285.1	s__JACQBZ01 sp016194285	80.1532	360	700	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__JACQBZ01;f__JACQBZ01;g__JACQBZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:59:32,063] [INFO] GTDB search result was written to GCA_016200255.1_ASM1620025v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:59:32,064] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:59:32,066] [INFO] DFAST_QC result json was written to GCA_016200255.1_ASM1620025v1_genomic.fna/dqc_result.json
[2023-06-30 10:59:32,066] [INFO] DFAST_QC completed!
[2023-06-30 10:59:32,066] [INFO] Total running time: 0h0m47s