[2023-06-08 03:42:22,792] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:22,795] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:22,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg42b9e429-5b77-45b5-961c-7fad7d2f8ae4/dqc_reference
[2023-06-08 03:42:24,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:24,103] [INFO] Task started: Prodigal
[2023-06-08 03:42:24,104] [INFO] Running command: gunzip -c /var/lib/cwl/stgd005cbc8-b180-4beb-bdef-c3198f46d7ac/GCA_902620175.1_AG-920-K08_genomic.fna.gz | prodigal -d GCA_902620175.1_AG-920-K08_genomic.fna/cds.fna -a GCA_902620175.1_AG-920-K08_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:25,238] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:25,238] [INFO] Task started: HMMsearch
[2023-06-08 03:42:25,238] [INFO] Running command: hmmsearch --tblout GCA_902620175.1_AG-920-K08_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42b9e429-5b77-45b5-961c-7fad7d2f8ae4/dqc_reference/reference_markers.hmm GCA_902620175.1_AG-920-K08_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:25,413] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:25,415] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd005cbc8-b180-4beb-bdef-c3198f46d7ac/GCA_902620175.1_AG-920-K08_genomic.fna.gz]
[2023-06-08 03:42:25,435] [INFO] Query marker FASTA was written to GCA_902620175.1_AG-920-K08_genomic.fna/markers.fasta
[2023-06-08 03:42:25,435] [INFO] Task started: Blastn
[2023-06-08 03:42:25,436] [INFO] Running command: blastn -query GCA_902620175.1_AG-920-K08_genomic.fna/markers.fasta -db /var/lib/cwl/stg42b9e429-5b77-45b5-961c-7fad7d2f8ae4/dqc_reference/reference_markers.fasta -out GCA_902620175.1_AG-920-K08_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:25,986] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:25,990] [INFO] Selected 4 target genomes.
[2023-06-08 03:42:25,991] [INFO] Target genome list was writen to GCA_902620175.1_AG-920-K08_genomic.fna/target_genomes.txt
[2023-06-08 03:42:25,993] [INFO] Task started: fastANI
[2023-06-08 03:42:25,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgd005cbc8-b180-4beb-bdef-c3198f46d7ac/GCA_902620175.1_AG-920-K08_genomic.fna.gz --refList GCA_902620175.1_AG-920-K08_genomic.fna/target_genomes.txt --output GCA_902620175.1_AG-920-K08_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:42:27,232] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:27,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42b9e429-5b77-45b5-961c-7fad7d2f8ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:42:27,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42b9e429-5b77-45b5-961c-7fad7d2f8ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:42:27,235] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:42:27,235] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:42:27,235] [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
--------------------------------------------------------------------------------
[2023-06-08 03:42:27,237] [INFO] DFAST Taxonomy check result was written to GCA_902620175.1_AG-920-K08_genomic.fna/tc_result.tsv
[2023-06-08 03:42:27,238] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:42:27,239] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:42:27,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42b9e429-5b77-45b5-961c-7fad7d2f8ae4/dqc_reference/checkm_data
[2023-06-08 03:42:27,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:42:27,255] [INFO] Task started: CheckM
[2023-06-08 03:42:27,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902620175.1_AG-920-K08_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902620175.1_AG-920-K08_genomic.fna/checkm_input GCA_902620175.1_AG-920-K08_genomic.fna/checkm_result
[2023-06-08 03:42:38,955] [INFO] Task succeeded: CheckM
[2023-06-08 03:42:38,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:42:38,972] [INFO] ===== Completeness check finished =====
[2023-06-08 03:42:38,973] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:42:38,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902620175.1_AG-920-K08_genomic.fna/markers.fasta)
[2023-06-08 03:42:38,973] [INFO] Task started: Blastn
[2023-06-08 03:42:38,974] [INFO] Running command: blastn -query GCA_902620175.1_AG-920-K08_genomic.fna/markers.fasta -db /var/lib/cwl/stg42b9e429-5b77-45b5-961c-7fad7d2f8ae4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902620175.1_AG-920-K08_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:39,789] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:39,798] [INFO] Selected 7 target genomes.
[2023-06-08 03:42:39,798] [INFO] Target genome list was writen to GCA_902620175.1_AG-920-K08_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:42:39,802] [INFO] Task started: fastANI
[2023-06-08 03:42:39,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgd005cbc8-b180-4beb-bdef-c3198f46d7ac/GCA_902620175.1_AG-920-K08_genomic.fna.gz --refList GCA_902620175.1_AG-920-K08_genomic.fna/target_genomes_gtdb.txt --output GCA_902620175.1_AG-920-K08_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:42:41,148] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:41,155] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-08 03:42:41,155] [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_902533795.1	s__Actinomarina sp902533795	95.4837	159	206	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.75	95.75	0.81	0.81	2	inconclusive
GCA_902604835.1	s__Actinomarina sp902604835	95.2775	152	206	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.34	95.34	0.81	0.81	2	inconclusive
GCA_902519845.1	s__Actinomarina sp902519845	94.6194	170	206	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.50	95.50	0.91	0.91	2	-
GCA_902571385.1	s__Actinomarina sp902571385	94.4027	168	206	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.95	95.63	0.85	0.83	4	-
GCA_902609285.1	s__Actinomarina sp902609285	93.3735	148	206	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282445.1	s__Actinomarina sp003282445	77.5408	64	206	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	-
--------------------------------------------------------------------------------
[2023-06-08 03:42:41,157] [INFO] GTDB search result was written to GCA_902620175.1_AG-920-K08_genomic.fna/result_gtdb.tsv
[2023-06-08 03:42:41,157] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:42:41,159] [INFO] DFAST_QC result json was written to GCA_902620175.1_AG-920-K08_genomic.fna/dqc_result.json
[2023-06-08 03:42:41,159] [INFO] DFAST_QC completed!
[2023-06-08 03:42:41,160] [INFO] Total running time: 0h0m18s