[2023-06-19 01:08:34,136] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:08:34,143] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:08:34,143] [INFO] DQC Reference Directory: /var/lib/cwl/stge9ab73c8-75ab-4519-8cf9-15a0c5ef221e/dqc_reference
[2023-06-19 01:08:35,665] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:08:35,666] [INFO] Task started: Prodigal
[2023-06-19 01:08:35,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f7139db-c575-4d46-8e93-5788db60a949/GCA_018882735.1_ASM1888273v1_genomic.fna.gz | prodigal -d GCA_018882735.1_ASM1888273v1_genomic.fna/cds.fna -a GCA_018882735.1_ASM1888273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:08:38,444] [INFO] Task succeeded: Prodigal
[2023-06-19 01:08:38,444] [INFO] Task started: HMMsearch
[2023-06-19 01:08:38,445] [INFO] Running command: hmmsearch --tblout GCA_018882735.1_ASM1888273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9ab73c8-75ab-4519-8cf9-15a0c5ef221e/dqc_reference/reference_markers.hmm GCA_018882735.1_ASM1888273v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:08:38,639] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:08:38,641] [INFO] Found 6/6 markers.
[2023-06-19 01:08:38,662] [INFO] Query marker FASTA was written to GCA_018882735.1_ASM1888273v1_genomic.fna/markers.fasta
[2023-06-19 01:08:38,662] [INFO] Task started: Blastn
[2023-06-19 01:08:38,662] [INFO] Running command: blastn -query GCA_018882735.1_ASM1888273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ab73c8-75ab-4519-8cf9-15a0c5ef221e/dqc_reference/reference_markers.fasta -out GCA_018882735.1_ASM1888273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:08:39,278] [INFO] Task succeeded: Blastn
[2023-06-19 01:08:39,281] [INFO] Selected 15 target genomes.
[2023-06-19 01:08:39,282] [INFO] Target genome list was writen to GCA_018882735.1_ASM1888273v1_genomic.fna/target_genomes.txt
[2023-06-19 01:08:39,284] [INFO] Task started: fastANI
[2023-06-19 01:08:39,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7139db-c575-4d46-8e93-5788db60a949/GCA_018882735.1_ASM1888273v1_genomic.fna.gz --refList GCA_018882735.1_ASM1888273v1_genomic.fna/target_genomes.txt --output GCA_018882735.1_ASM1888273v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:08:45,426] [INFO] Task succeeded: fastANI
[2023-06-19 01:08:45,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9ab73c8-75ab-4519-8cf9-15a0c5ef221e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:08:45,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9ab73c8-75ab-4519-8cf9-15a0c5ef221e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:08:45,429] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:08:45,429] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 01:08:45,429] [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 01:08:45,431] [INFO] DFAST Taxonomy check result was written to GCA_018882735.1_ASM1888273v1_genomic.fna/tc_result.tsv
[2023-06-19 01:08:45,431] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:08:45,431] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:08:45,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9ab73c8-75ab-4519-8cf9-15a0c5ef221e/dqc_reference/checkm_data
[2023-06-19 01:08:45,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:08:45,462] [INFO] Task started: CheckM
[2023-06-19 01:08:45,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018882735.1_ASM1888273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018882735.1_ASM1888273v1_genomic.fna/checkm_input GCA_018882735.1_ASM1888273v1_genomic.fna/checkm_result
[2023-06-19 01:09:03,036] [INFO] Task succeeded: CheckM
[2023-06-19 01:09:03,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 01:09:03,071] [INFO] ===== Completeness check finished =====
[2023-06-19 01:09:03,072] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:09:03,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018882735.1_ASM1888273v1_genomic.fna/markers.fasta)
[2023-06-19 01:09:03,072] [INFO] Task started: Blastn
[2023-06-19 01:09:03,072] [INFO] Running command: blastn -query GCA_018882735.1_ASM1888273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ab73c8-75ab-4519-8cf9-15a0c5ef221e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018882735.1_ASM1888273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:09:03,966] [INFO] Task succeeded: Blastn
[2023-06-19 01:09:03,971] [INFO] Selected 10 target genomes.
[2023-06-19 01:09:03,972] [INFO] Target genome list was writen to GCA_018882735.1_ASM1888273v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:09:03,979] [INFO] Task started: fastANI
[2023-06-19 01:09:03,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7139db-c575-4d46-8e93-5788db60a949/GCA_018882735.1_ASM1888273v1_genomic.fna.gz --refList GCA_018882735.1_ASM1888273v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018882735.1_ASM1888273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:09:06,380] [INFO] Task succeeded: fastANI
[2023-06-19 01:09:06,390] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:09:06,390] [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_018882735.1	s__MAG-120802 sp018882735	100.0	376	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016870855.1	s__MAG-120802 sp016870855	87.3623	258	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010023045.1	s__MAG-120802 sp010023045	85.035	275	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	98.95	98.70	0.90	0.88	12	-
GCA_016870835.1	s__MAG-120802 sp016870835	80.068	140	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032085.1	s__MAG-120802 sp010032085	78.7401	84	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	99.10	99.05	0.87	0.80	3	-
GCA_018882745.1	s__MAG-120802 sp018882745	78.286	92	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870975.1	s__MAG-120802 sp016870975	78.0329	77	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569145.1	s__MAG-120802 sp003569145	77.716	82	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	99.02	99.02	0.96	0.96	2	-
GCA_009927705.1	s__MAG-120802 sp009927705	77.0715	53	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	99.07	99.07	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-19 01:09:06,392] [INFO] GTDB search result was written to GCA_018882735.1_ASM1888273v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:09:06,393] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:09:06,400] [INFO] DFAST_QC result json was written to GCA_018882735.1_ASM1888273v1_genomic.fna/dqc_result.json
[2023-06-19 01:09:06,400] [INFO] DFAST_QC completed!
[2023-06-19 01:09:06,401] [INFO] Total running time: 0h0m32s