[2023-06-29 14:02:13,376] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:02:13,380] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:02:13,381] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2ca5b96-7969-4004-b44e-141feac493f5/dqc_reference
[2023-06-29 14:02:14,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:02:14,739] [INFO] Task started: Prodigal
[2023-06-29 14:02:14,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg646910b4-2008-4cef-abd3-23c01b44bcab/GCA_021738405.1_ASM2173840v1_genomic.fna.gz | prodigal -d GCA_021738405.1_ASM2173840v1_genomic.fna/cds.fna -a GCA_021738405.1_ASM2173840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:02:26,491] [INFO] Task succeeded: Prodigal
[2023-06-29 14:02:26,491] [INFO] Task started: HMMsearch
[2023-06-29 14:02:26,491] [INFO] Running command: hmmsearch --tblout GCA_021738405.1_ASM2173840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2ca5b96-7969-4004-b44e-141feac493f5/dqc_reference/reference_markers.hmm GCA_021738405.1_ASM2173840v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:02:26,713] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:02:26,715] [INFO] Found 6/6 markers.
[2023-06-29 14:02:26,740] [INFO] Query marker FASTA was written to GCA_021738405.1_ASM2173840v1_genomic.fna/markers.fasta
[2023-06-29 14:02:26,741] [INFO] Task started: Blastn
[2023-06-29 14:02:26,741] [INFO] Running command: blastn -query GCA_021738405.1_ASM2173840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2ca5b96-7969-4004-b44e-141feac493f5/dqc_reference/reference_markers.fasta -out GCA_021738405.1_ASM2173840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:02:27,338] [INFO] Task succeeded: Blastn
[2023-06-29 14:02:27,343] [INFO] Selected 30 target genomes.
[2023-06-29 14:02:27,343] [INFO] Target genome list was writen to GCA_021738405.1_ASM2173840v1_genomic.fna/target_genomes.txt
[2023-06-29 14:02:27,356] [INFO] Task started: fastANI
[2023-06-29 14:02:27,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg646910b4-2008-4cef-abd3-23c01b44bcab/GCA_021738405.1_ASM2173840v1_genomic.fna.gz --refList GCA_021738405.1_ASM2173840v1_genomic.fna/target_genomes.txt --output GCA_021738405.1_ASM2173840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:02:48,072] [INFO] Task succeeded: fastANI
[2023-06-29 14:02:48,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2ca5b96-7969-4004-b44e-141feac493f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:02:48,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2ca5b96-7969-4004-b44e-141feac493f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:02:48,076] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:02:48,076] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:02:48,076] [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 14:02:48,078] [INFO] DFAST Taxonomy check result was written to GCA_021738405.1_ASM2173840v1_genomic.fna/tc_result.tsv
[2023-06-29 14:02:48,079] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:02:48,079] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:02:48,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2ca5b96-7969-4004-b44e-141feac493f5/dqc_reference/checkm_data
[2023-06-29 14:02:48,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:02:48,111] [INFO] Task started: CheckM
[2023-06-29 14:02:48,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021738405.1_ASM2173840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021738405.1_ASM2173840v1_genomic.fna/checkm_input GCA_021738405.1_ASM2173840v1_genomic.fna/checkm_result
[2023-06-29 14:03:25,958] [INFO] Task succeeded: CheckM
[2023-06-29 14:03:25,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:03:25,989] [INFO] ===== Completeness check finished =====
[2023-06-29 14:03:25,990] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:03:25,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021738405.1_ASM2173840v1_genomic.fna/markers.fasta)
[2023-06-29 14:03:25,991] [INFO] Task started: Blastn
[2023-06-29 14:03:25,991] [INFO] Running command: blastn -query GCA_021738405.1_ASM2173840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2ca5b96-7969-4004-b44e-141feac493f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_021738405.1_ASM2173840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:03:26,793] [INFO] Task succeeded: Blastn
[2023-06-29 14:03:26,799] [INFO] Selected 20 target genomes.
[2023-06-29 14:03:26,799] [INFO] Target genome list was writen to GCA_021738405.1_ASM2173840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:03:26,831] [INFO] Task started: fastANI
[2023-06-29 14:03:26,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg646910b4-2008-4cef-abd3-23c01b44bcab/GCA_021738405.1_ASM2173840v1_genomic.fna.gz --refList GCA_021738405.1_ASM2173840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021738405.1_ASM2173840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:03:38,867] [INFO] Task succeeded: fastANI
[2023-06-29 14:03:38,880] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:03:38,880] [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_004295165.1	s__UBA952 sp004295165	90.1508	339	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002293185.1	s__UBA952 sp002293185	79.8941	359	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872115.1	s__UBA952 sp016872115	79.304	336	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478565.1	s__UBA952 sp002478565	78.5076	270	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.96	99.96	0.95	0.95	2	-
GCA_017983465.1	s__UBA952 sp017983465	77.3427	74	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:03:38,883] [INFO] GTDB search result was written to GCA_021738405.1_ASM2173840v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:03:38,884] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:03:38,887] [INFO] DFAST_QC result json was written to GCA_021738405.1_ASM2173840v1_genomic.fna/dqc_result.json
[2023-06-29 14:03:38,888] [INFO] DFAST_QC completed!
[2023-06-29 14:03:38,888] [INFO] Total running time: 0h1m26s