[2023-06-27 06:42:21,071] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:42:21,074] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:42:21,074] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6a7e8a0-0eed-435c-acd4-7f2b652d611d/dqc_reference
[2023-06-27 06:42:22,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:42:22,307] [INFO] Task started: Prodigal
[2023-06-27 06:42:22,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg4462d3de-3253-46a8-b9cb-5257300be07e/GCA_027731335.1_ASM2773133v1_genomic.fna.gz | prodigal -d GCA_027731335.1_ASM2773133v1_genomic.fna/cds.fna -a GCA_027731335.1_ASM2773133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:42:23,749] [INFO] Task succeeded: Prodigal
[2023-06-27 06:42:23,750] [INFO] Task started: HMMsearch
[2023-06-27 06:42:23,750] [INFO] Running command: hmmsearch --tblout GCA_027731335.1_ASM2773133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6a7e8a0-0eed-435c-acd4-7f2b652d611d/dqc_reference/reference_markers.hmm GCA_027731335.1_ASM2773133v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:42:23,954] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:42:23,956] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4462d3de-3253-46a8-b9cb-5257300be07e/GCA_027731335.1_ASM2773133v1_genomic.fna.gz]
[2023-06-27 06:42:23,974] [INFO] Query marker FASTA was written to GCA_027731335.1_ASM2773133v1_genomic.fna/markers.fasta
[2023-06-27 06:42:23,975] [INFO] Task started: Blastn
[2023-06-27 06:42:23,975] [INFO] Running command: blastn -query GCA_027731335.1_ASM2773133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6a7e8a0-0eed-435c-acd4-7f2b652d611d/dqc_reference/reference_markers.fasta -out GCA_027731335.1_ASM2773133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:42:24,468] [INFO] Task succeeded: Blastn
[2023-06-27 06:42:24,473] [INFO] Selected 16 target genomes.
[2023-06-27 06:42:24,473] [INFO] Target genome list was writen to GCA_027731335.1_ASM2773133v1_genomic.fna/target_genomes.txt
[2023-06-27 06:42:24,479] [INFO] Task started: fastANI
[2023-06-27 06:42:24,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg4462d3de-3253-46a8-b9cb-5257300be07e/GCA_027731335.1_ASM2773133v1_genomic.fna.gz --refList GCA_027731335.1_ASM2773133v1_genomic.fna/target_genomes.txt --output GCA_027731335.1_ASM2773133v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:42:31,001] [INFO] Task succeeded: fastANI
[2023-06-27 06:42:31,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6a7e8a0-0eed-435c-acd4-7f2b652d611d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:42:31,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6a7e8a0-0eed-435c-acd4-7f2b652d611d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:42:31,005] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:42:31,005] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:42:31,005] [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
--------------------------------------------------------------------------------
[2023-06-27 06:42:31,008] [INFO] DFAST Taxonomy check result was written to GCA_027731335.1_ASM2773133v1_genomic.fna/tc_result.tsv
[2023-06-27 06:42:31,009] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:42:31,009] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:42:31,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6a7e8a0-0eed-435c-acd4-7f2b652d611d/dqc_reference/checkm_data
[2023-06-27 06:42:31,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:42:31,031] [INFO] Task started: CheckM
[2023-06-27 06:42:31,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027731335.1_ASM2773133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027731335.1_ASM2773133v1_genomic.fna/checkm_input GCA_027731335.1_ASM2773133v1_genomic.fna/checkm_result
[2023-06-27 06:42:43,829] [INFO] Task succeeded: CheckM
[2023-06-27 06:42:43,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:42:43,850] [INFO] ===== Completeness check finished =====
[2023-06-27 06:42:43,851] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:42:43,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027731335.1_ASM2773133v1_genomic.fna/markers.fasta)
[2023-06-27 06:42:43,852] [INFO] Task started: Blastn
[2023-06-27 06:42:43,852] [INFO] Running command: blastn -query GCA_027731335.1_ASM2773133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6a7e8a0-0eed-435c-acd4-7f2b652d611d/dqc_reference/reference_markers_gtdb.fasta -out GCA_027731335.1_ASM2773133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:42:44,351] [INFO] Task succeeded: Blastn
[2023-06-27 06:42:44,356] [INFO] Selected 9 target genomes.
[2023-06-27 06:42:44,356] [INFO] Target genome list was writen to GCA_027731335.1_ASM2773133v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:42:44,365] [INFO] Task started: fastANI
[2023-06-27 06:42:44,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg4462d3de-3253-46a8-b9cb-5257300be07e/GCA_027731335.1_ASM2773133v1_genomic.fna.gz --refList GCA_027731335.1_ASM2773133v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027731335.1_ASM2773133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:42:46,153] [INFO] Task succeeded: fastANI
[2023-06-27 06:42:46,171] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:42:46,172] [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_016777845.1	s__Actinomarina sp016777845	98.7786	170	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004213405.1	s__Actinomarina sp004213405	92.3456	152	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580215.1	s__Actinomarina sp902580215	90.9428	200	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.48	95.05	0.79	0.77	5	-
GCA_902593475.1	s__Actinomarina sp902593475	90.3763	157	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599555.1	s__Actinomarina sp902599555	90.3503	199	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610815.1	s__Actinomarina sp902610815	88.8814	209	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576605.1	s__Actinomarina sp902576605	88.5662	176	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628045.1	s__Actinomarina sp902628045	85.8514	169	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622665.1	s__Actinomarina sp902622665	85.6624	187	259	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:42:46,174] [INFO] GTDB search result was written to GCA_027731335.1_ASM2773133v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:42:46,175] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:42:46,201] [INFO] DFAST_QC result json was written to GCA_027731335.1_ASM2773133v1_genomic.fna/dqc_result.json
[2023-06-27 06:42:46,202] [INFO] DFAST_QC completed!
[2023-06-27 06:42:46,202] [INFO] Total running time: 0h0m25s