[2023-06-29 03:47:16,557] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:47:16,560] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:47:16,561] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0b88264-787b-4478-964d-be69a64eb042/dqc_reference
[2023-06-29 03:47:18,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:47:18,930] [INFO] Task started: Prodigal
[2023-06-29 03:47:18,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg545483e4-c0b1-434e-b6d5-7a5c1b78888d/GCA_020626765.1_ASM2062676v1_genomic.fna.gz | prodigal -d GCA_020626765.1_ASM2062676v1_genomic.fna/cds.fna -a GCA_020626765.1_ASM2062676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:47:22,229] [INFO] Task succeeded: Prodigal
[2023-06-29 03:47:22,229] [INFO] Task started: HMMsearch
[2023-06-29 03:47:22,229] [INFO] Running command: hmmsearch --tblout GCA_020626765.1_ASM2062676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0b88264-787b-4478-964d-be69a64eb042/dqc_reference/reference_markers.hmm GCA_020626765.1_ASM2062676v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:47:22,519] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:47:22,521] [INFO] Found 6/6 markers.
[2023-06-29 03:47:22,546] [INFO] Query marker FASTA was written to GCA_020626765.1_ASM2062676v1_genomic.fna/markers.fasta
[2023-06-29 03:47:22,547] [INFO] Task started: Blastn
[2023-06-29 03:47:22,547] [INFO] Running command: blastn -query GCA_020626765.1_ASM2062676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0b88264-787b-4478-964d-be69a64eb042/dqc_reference/reference_markers.fasta -out GCA_020626765.1_ASM2062676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:47:23,335] [INFO] Task succeeded: Blastn
[2023-06-29 03:47:23,341] [INFO] Selected 67 target genomes.
[2023-06-29 03:47:23,341] [INFO] Target genome list was writen to GCA_020626765.1_ASM2062676v1_genomic.fna/target_genomes.txt
[2023-06-29 03:47:23,379] [INFO] Task started: fastANI
[2023-06-29 03:47:23,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg545483e4-c0b1-434e-b6d5-7a5c1b78888d/GCA_020626765.1_ASM2062676v1_genomic.fna.gz --refList GCA_020626765.1_ASM2062676v1_genomic.fna/target_genomes.txt --output GCA_020626765.1_ASM2062676v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:47:49,647] [INFO] Task succeeded: fastANI
[2023-06-29 03:47:49,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0b88264-787b-4478-964d-be69a64eb042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:47:49,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0b88264-787b-4478-964d-be69a64eb042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:47:49,650] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:47:49,650] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 03:47:49,651] [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
--------------------------------------------------------------------------------
[2023-06-29 03:47:49,653] [INFO] DFAST Taxonomy check result was written to GCA_020626765.1_ASM2062676v1_genomic.fna/tc_result.tsv
[2023-06-29 03:47:49,653] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:47:49,654] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:47:49,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0b88264-787b-4478-964d-be69a64eb042/dqc_reference/checkm_data
[2023-06-29 03:47:49,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:47:49,706] [INFO] Task started: CheckM
[2023-06-29 03:47:49,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020626765.1_ASM2062676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020626765.1_ASM2062676v1_genomic.fna/checkm_input GCA_020626765.1_ASM2062676v1_genomic.fna/checkm_result
[2023-06-29 03:48:13,667] [INFO] Task succeeded: CheckM
[2023-06-29 03:48:13,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 140.18%
Strain heterogeneity: 6.11%
--------------------------------------------------------------------------------
[2023-06-29 03:48:13,709] [INFO] ===== Completeness check finished =====
[2023-06-29 03:48:13,710] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:48:13,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020626765.1_ASM2062676v1_genomic.fna/markers.fasta)
[2023-06-29 03:48:13,711] [INFO] Task started: Blastn
[2023-06-29 03:48:13,711] [INFO] Running command: blastn -query GCA_020626765.1_ASM2062676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0b88264-787b-4478-964d-be69a64eb042/dqc_reference/reference_markers_gtdb.fasta -out GCA_020626765.1_ASM2062676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:48:14,582] [INFO] Task succeeded: Blastn
[2023-06-29 03:48:14,589] [INFO] Selected 59 target genomes.
[2023-06-29 03:48:14,590] [INFO] Target genome list was writen to GCA_020626765.1_ASM2062676v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:48:14,646] [INFO] Task started: fastANI
[2023-06-29 03:48:14,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg545483e4-c0b1-434e-b6d5-7a5c1b78888d/GCA_020626765.1_ASM2062676v1_genomic.fna.gz --refList GCA_020626765.1_ASM2062676v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020626765.1_ASM2062676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:48:29,755] [INFO] Task succeeded: fastANI
[2023-06-29 03:48:29,772] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:48:29,773] [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_017460175.1	s__UBA3789 sp017460175	80.79	104	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541885.1	s__UBA3789 sp017541885	80.6412	112	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783435.1	s__UBA3789 sp902783435	80.4963	111	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369415.1	s__UBA3789 sp002369415	80.4029	113	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768065.1	s__UBA3789 sp902768065	80.1947	102	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409785.1	s__CAG-877 sp017409785	80.0972	89	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293205.1	s__CAG-877 sp016293205	79.9778	88	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543055.1	s__UBA3789 sp900543055	79.798	108	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.54	97.21	0.78	0.56	4	-
GCA_017622175.1	s__CAG-877 sp017622175	79.791	101	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433415.1	s__UBA3789 sp017433415	79.7862	90	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780585.1	s__UBA3789 sp902780585	79.7432	97	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.24	98.24	0.79	0.79	2	-
GCA_902780395.1	s__UBA3789 sp902780395	79.4513	111	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550205.1	s__UBA3789 sp017550205	79.41	70	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589335.1	s__UBA3789 sp910589335	79.2981	94	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793315.1	s__UBA3789 sp902793315	79.0244	92	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.53	98.26	0.86	0.76	3	-
GCA_017432665.1	s__UBA3789 sp017432665	78.9516	86	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783315.1	s__UBA3789 sp902783315	78.7222	82	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796215.1	s__UBA3789 sp902796215	78.533	81	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425325.1	s__UBA5578 sp002425325	78.065	54	332	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:48:29,774] [INFO] GTDB search result was written to GCA_020626765.1_ASM2062676v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:48:29,775] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:48:29,779] [INFO] DFAST_QC result json was written to GCA_020626765.1_ASM2062676v1_genomic.fna/dqc_result.json
[2023-06-29 03:48:29,779] [INFO] DFAST_QC completed!
[2023-06-29 03:48:29,780] [INFO] Total running time: 0h1m13s