[2023-06-19 06:19:08,124] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:19:08,142] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:19:08,142] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f8378b0-3c9c-4d6f-a7b9-2255984cb1f0/dqc_reference
[2023-06-19 06:19:09,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:19:09,608] [INFO] Task started: Prodigal
[2023-06-19 06:19:09,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg5555a910-e069-4660-8437-7bf74549deb0/GCA_018716565.1_ASM1871656v1_genomic.fna.gz | prodigal -d GCA_018716565.1_ASM1871656v1_genomic.fna/cds.fna -a GCA_018716565.1_ASM1871656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:19:12,963] [INFO] Task succeeded: Prodigal
[2023-06-19 06:19:12,964] [INFO] Task started: HMMsearch
[2023-06-19 06:19:12,964] [INFO] Running command: hmmsearch --tblout GCA_018716565.1_ASM1871656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f8378b0-3c9c-4d6f-a7b9-2255984cb1f0/dqc_reference/reference_markers.hmm GCA_018716565.1_ASM1871656v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:19:13,183] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:19:13,188] [INFO] Found 6/6 markers.
[2023-06-19 06:19:13,216] [INFO] Query marker FASTA was written to GCA_018716565.1_ASM1871656v1_genomic.fna/markers.fasta
[2023-06-19 06:19:13,217] [INFO] Task started: Blastn
[2023-06-19 06:19:13,217] [INFO] Running command: blastn -query GCA_018716565.1_ASM1871656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f8378b0-3c9c-4d6f-a7b9-2255984cb1f0/dqc_reference/reference_markers.fasta -out GCA_018716565.1_ASM1871656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:13,795] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:13,799] [INFO] Selected 20 target genomes.
[2023-06-19 06:19:13,800] [INFO] Target genome list was writen to GCA_018716565.1_ASM1871656v1_genomic.fna/target_genomes.txt
[2023-06-19 06:19:13,805] [INFO] Task started: fastANI
[2023-06-19 06:19:13,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg5555a910-e069-4660-8437-7bf74549deb0/GCA_018716565.1_ASM1871656v1_genomic.fna.gz --refList GCA_018716565.1_ASM1871656v1_genomic.fna/target_genomes.txt --output GCA_018716565.1_ASM1871656v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:19:21,397] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:21,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f8378b0-3c9c-4d6f-a7b9-2255984cb1f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:19:21,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f8378b0-3c9c-4d6f-a7b9-2255984cb1f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:19:21,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:19:21,406] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 06:19:21,406] [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 06:19:21,408] [INFO] DFAST Taxonomy check result was written to GCA_018716565.1_ASM1871656v1_genomic.fna/tc_result.tsv
[2023-06-19 06:19:21,409] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:19:21,409] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:19:21,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f8378b0-3c9c-4d6f-a7b9-2255984cb1f0/dqc_reference/checkm_data
[2023-06-19 06:19:21,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:19:21,440] [INFO] Task started: CheckM
[2023-06-19 06:19:21,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018716565.1_ASM1871656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018716565.1_ASM1871656v1_genomic.fna/checkm_input GCA_018716565.1_ASM1871656v1_genomic.fna/checkm_result
[2023-06-19 06:19:39,408] [INFO] Task succeeded: CheckM
[2023-06-19 06:19:39,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:19:39,438] [INFO] ===== Completeness check finished =====
[2023-06-19 06:19:39,438] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:19:39,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018716565.1_ASM1871656v1_genomic.fna/markers.fasta)
[2023-06-19 06:19:39,439] [INFO] Task started: Blastn
[2023-06-19 06:19:39,439] [INFO] Running command: blastn -query GCA_018716565.1_ASM1871656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f8378b0-3c9c-4d6f-a7b9-2255984cb1f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018716565.1_ASM1871656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:40,218] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:40,225] [INFO] Selected 11 target genomes.
[2023-06-19 06:19:40,225] [INFO] Target genome list was writen to GCA_018716565.1_ASM1871656v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:19:40,234] [INFO] Task started: fastANI
[2023-06-19 06:19:40,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg5555a910-e069-4660-8437-7bf74549deb0/GCA_018716565.1_ASM1871656v1_genomic.fna.gz --refList GCA_018716565.1_ASM1871656v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018716565.1_ASM1871656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:19:44,924] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:44,939] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:19:44,940] [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_018716565.1	s__Avigastranaerophilus faecigallinarum	100.0	634	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910583875.1	s__Avigastranaerophilus sp910583875	79.5971	342	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015152515.1	s__Avigastranaerophilus sp015152515	79.3104	242	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017467305.1	s__Avigastranaerophilus sp017467305	79.0254	248	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017396025.1	s__Avigastranaerophilus sp017396025	78.9174	210	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470245.1	s__Avigastranaerophilus sp017470245	78.7269	265	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282705.1	s__Avigastranaerophilus sp016282705	78.642	231	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235825.1	s__Avigastranaerophilus sp905235825	76.8659	175	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234915.1	s__Avigastranaerophilus sp905234915	76.7026	158	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775025.1	s__CAG-196 sp902775025	76.1447	57	642	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:19:44,942] [INFO] GTDB search result was written to GCA_018716565.1_ASM1871656v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:19:44,943] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:19:44,946] [INFO] DFAST_QC result json was written to GCA_018716565.1_ASM1871656v1_genomic.fna/dqc_result.json
[2023-06-19 06:19:44,946] [INFO] DFAST_QC completed!
[2023-06-19 06:19:44,947] [INFO] Total running time: 0h0m37s