[2023-06-28 03:48:59,112] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:48:59,114] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:48:59,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg4351992c-b79c-4efd-9bd2-00bc3226cbee/dqc_reference
[2023-06-28 03:49:00,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:49:00,327] [INFO] Task started: Prodigal
[2023-06-28 03:49:00,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg03667dcd-58da-4976-b068-c2987f9aea2e/GCA_017880715.1_ASM1788071v1_genomic.fna.gz | prodigal -d GCA_017880715.1_ASM1788071v1_genomic.fna/cds.fna -a GCA_017880715.1_ASM1788071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:49:08,300] [INFO] Task succeeded: Prodigal
[2023-06-28 03:49:08,300] [INFO] Task started: HMMsearch
[2023-06-28 03:49:08,301] [INFO] Running command: hmmsearch --tblout GCA_017880715.1_ASM1788071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4351992c-b79c-4efd-9bd2-00bc3226cbee/dqc_reference/reference_markers.hmm GCA_017880715.1_ASM1788071v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:49:08,527] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:49:08,529] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg03667dcd-58da-4976-b068-c2987f9aea2e/GCA_017880715.1_ASM1788071v1_genomic.fna.gz]
[2023-06-28 03:49:08,563] [INFO] Query marker FASTA was written to GCA_017880715.1_ASM1788071v1_genomic.fna/markers.fasta
[2023-06-28 03:49:08,563] [INFO] Task started: Blastn
[2023-06-28 03:49:08,564] [INFO] Running command: blastn -query GCA_017880715.1_ASM1788071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4351992c-b79c-4efd-9bd2-00bc3226cbee/dqc_reference/reference_markers.fasta -out GCA_017880715.1_ASM1788071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:49:09,118] [INFO] Task succeeded: Blastn
[2023-06-28 03:49:09,124] [INFO] Selected 8 target genomes.
[2023-06-28 03:49:09,125] [INFO] Target genome list was writen to GCA_017880715.1_ASM1788071v1_genomic.fna/target_genomes.txt
[2023-06-28 03:49:09,128] [INFO] Task started: fastANI
[2023-06-28 03:49:09,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg03667dcd-58da-4976-b068-c2987f9aea2e/GCA_017880715.1_ASM1788071v1_genomic.fna.gz --refList GCA_017880715.1_ASM1788071v1_genomic.fna/target_genomes.txt --output GCA_017880715.1_ASM1788071v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:49:15,234] [INFO] Task succeeded: fastANI
[2023-06-28 03:49:15,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4351992c-b79c-4efd-9bd2-00bc3226cbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:49:15,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4351992c-b79c-4efd-9bd2-00bc3226cbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:49:15,237] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:49:15,237] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 03:49:15,237] [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
--------------------------------------------------------------------------------
[2023-06-28 03:49:15,240] [INFO] DFAST Taxonomy check result was written to GCA_017880715.1_ASM1788071v1_genomic.fna/tc_result.tsv
[2023-06-28 03:49:15,240] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:49:15,241] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:49:15,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4351992c-b79c-4efd-9bd2-00bc3226cbee/dqc_reference/checkm_data
[2023-06-28 03:49:15,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:49:15,277] [INFO] Task started: CheckM
[2023-06-28 03:49:15,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017880715.1_ASM1788071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017880715.1_ASM1788071v1_genomic.fna/checkm_input GCA_017880715.1_ASM1788071v1_genomic.fna/checkm_result
[2023-06-28 03:49:43,496] [INFO] Task succeeded: CheckM
[2023-06-28 03:49:43,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 03:49:43,521] [INFO] ===== Completeness check finished =====
[2023-06-28 03:49:43,522] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:49:43,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017880715.1_ASM1788071v1_genomic.fna/markers.fasta)
[2023-06-28 03:49:43,522] [INFO] Task started: Blastn
[2023-06-28 03:49:43,522] [INFO] Running command: blastn -query GCA_017880715.1_ASM1788071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4351992c-b79c-4efd-9bd2-00bc3226cbee/dqc_reference/reference_markers_gtdb.fasta -out GCA_017880715.1_ASM1788071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:49:44,228] [INFO] Task succeeded: Blastn
[2023-06-28 03:49:44,233] [INFO] Selected 12 target genomes.
[2023-06-28 03:49:44,233] [INFO] Target genome list was writen to GCA_017880715.1_ASM1788071v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:49:44,240] [INFO] Task started: fastANI
[2023-06-28 03:49:44,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg03667dcd-58da-4976-b068-c2987f9aea2e/GCA_017880715.1_ASM1788071v1_genomic.fna.gz --refList GCA_017880715.1_ASM1788071v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017880715.1_ASM1788071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:49:55,347] [INFO] Task succeeded: fastANI
[2023-06-28 03:49:55,361] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 03:49:55,361] [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_017880715.1	s__JADGRT01 sp017880715	100.0	797	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JADGRT01;g__JADGRT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003152225.1	s__PALSA-1440 sp003152225	76.0883	72	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011327785.1	s__DSVZ01 sp011327785	75.8886	81	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903895255.1	s__UBA11358 sp903895255	75.8126	62	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.95	99.95	0.98	0.98	2	-
GCA_903912925.1	s__PALSA-1440 sp903912925	75.7348	77	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930565.1	s__CAIXFN01 sp903930565	75.7094	56	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Pedosphaeraceae;g__CAIXFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845125.1	s__CAIMWS01 sp903845125	75.6637	68	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1319;g__CAIMWS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235585.1	s__JACRJY01 sp016235585	75.5086	65	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJY01;g__JACRJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872345.1	s__UBA11358 sp903872345	75.0128	69	816	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	100.00	100.00	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-06-28 03:49:55,363] [INFO] GTDB search result was written to GCA_017880715.1_ASM1788071v1_genomic.fna/result_gtdb.tsv
[2023-06-28 03:49:55,364] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:49:55,366] [INFO] DFAST_QC result json was written to GCA_017880715.1_ASM1788071v1_genomic.fna/dqc_result.json
[2023-06-28 03:49:55,366] [INFO] DFAST_QC completed!
[2023-06-28 03:49:55,367] [INFO] Total running time: 0h0m56s