[2023-06-18 14:34:42,679] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:34:42,682] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:34:42,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg36c68e34-797e-4818-bc23-d59006de6848/dqc_reference
[2023-06-18 14:34:44,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:34:44,420] [INFO] Task started: Prodigal
[2023-06-18 14:34:44,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b94eb03-72dd-4a73-b369-4df88a168ab3/GCA_018646345.1_ASM1864634v1_genomic.fna.gz | prodigal -d GCA_018646345.1_ASM1864634v1_genomic.fna/cds.fna -a GCA_018646345.1_ASM1864634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:34:48,340] [INFO] Task succeeded: Prodigal
[2023-06-18 14:34:48,340] [INFO] Task started: HMMsearch
[2023-06-18 14:34:48,340] [INFO] Running command: hmmsearch --tblout GCA_018646345.1_ASM1864634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36c68e34-797e-4818-bc23-d59006de6848/dqc_reference/reference_markers.hmm GCA_018646345.1_ASM1864634v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:34:48,531] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:34:48,535] [INFO] Found 6/6 markers.
[2023-06-18 14:34:48,555] [INFO] Query marker FASTA was written to GCA_018646345.1_ASM1864634v1_genomic.fna/markers.fasta
[2023-06-18 14:34:48,555] [INFO] Task started: Blastn
[2023-06-18 14:34:48,556] [INFO] Running command: blastn -query GCA_018646345.1_ASM1864634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36c68e34-797e-4818-bc23-d59006de6848/dqc_reference/reference_markers.fasta -out GCA_018646345.1_ASM1864634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:34:49,120] [INFO] Task succeeded: Blastn
[2023-06-18 14:34:49,130] [INFO] Selected 30 target genomes.
[2023-06-18 14:34:49,130] [INFO] Target genome list was writen to GCA_018646345.1_ASM1864634v1_genomic.fna/target_genomes.txt
[2023-06-18 14:34:49,134] [INFO] Task started: fastANI
[2023-06-18 14:34:49,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b94eb03-72dd-4a73-b369-4df88a168ab3/GCA_018646345.1_ASM1864634v1_genomic.fna.gz --refList GCA_018646345.1_ASM1864634v1_genomic.fna/target_genomes.txt --output GCA_018646345.1_ASM1864634v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:35:05,492] [INFO] Task succeeded: fastANI
[2023-06-18 14:35:05,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36c68e34-797e-4818-bc23-d59006de6848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:35:05,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36c68e34-797e-4818-bc23-d59006de6848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:35:05,497] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:35:05,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 14:35:05,498] [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
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	75.712	50	469	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	75.6469	50	469	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 14:35:05,500] [INFO] DFAST Taxonomy check result was written to GCA_018646345.1_ASM1864634v1_genomic.fna/tc_result.tsv
[2023-06-18 14:35:05,502] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:35:05,503] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:35:05,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36c68e34-797e-4818-bc23-d59006de6848/dqc_reference/checkm_data
[2023-06-18 14:35:05,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:35:05,523] [INFO] Task started: CheckM
[2023-06-18 14:35:05,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018646345.1_ASM1864634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018646345.1_ASM1864634v1_genomic.fna/checkm_input GCA_018646345.1_ASM1864634v1_genomic.fna/checkm_result
[2023-06-18 14:35:23,743] [INFO] Task succeeded: CheckM
[2023-06-18 14:35:23,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 14:35:23,767] [INFO] ===== Completeness check finished =====
[2023-06-18 14:35:23,767] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:35:23,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018646345.1_ASM1864634v1_genomic.fna/markers.fasta)
[2023-06-18 14:35:23,768] [INFO] Task started: Blastn
[2023-06-18 14:35:23,768] [INFO] Running command: blastn -query GCA_018646345.1_ASM1864634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36c68e34-797e-4818-bc23-d59006de6848/dqc_reference/reference_markers_gtdb.fasta -out GCA_018646345.1_ASM1864634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:35:24,522] [INFO] Task succeeded: Blastn
[2023-06-18 14:35:24,528] [INFO] Selected 21 target genomes.
[2023-06-18 14:35:24,529] [INFO] Target genome list was writen to GCA_018646345.1_ASM1864634v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:35:24,558] [INFO] Task started: fastANI
[2023-06-18 14:35:24,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b94eb03-72dd-4a73-b369-4df88a168ab3/GCA_018646345.1_ASM1864634v1_genomic.fna.gz --refList GCA_018646345.1_ASM1864634v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018646345.1_ASM1864634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:35:31,073] [INFO] Task succeeded: fastANI
[2023-06-18 14:35:31,084] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 14:35:31,084] [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_018657955.1	s__GCA-2700405 sp018657955	99.9478	452	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	99.95	99.87	0.95	0.89	9	conclusive
GCA_014239895.1	s__GCA-2700405 sp014239895	90.6302	267	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512065.1	s__GCA-2700405 sp902512065	82.5521	303	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213965.1	s__GCA-2700405 sp004213965	82.0642	277	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700405.1	s__GCA-2700405 sp002700405	81.7358	256	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	77.1192	65	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902608795.1	s__MED-G13 sp902608795	76.9438	61	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515565.1	s__SGZJ01 sp902515565	76.8737	77	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	76.8634	92	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526075.1	s__MED-G13 sp902526075	76.8459	62	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902581145.1	s__MED-G13 sp902581145	76.7883	76	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691265.1	s__MED-G13 sp002691265	76.7609	77	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.61	95.49	0.82	0.79	4	-
GCA_018674025.1	s__SGZJ01 sp018674025	75.8615	71	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 14:35:31,086] [INFO] GTDB search result was written to GCA_018646345.1_ASM1864634v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:35:31,091] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:35:31,094] [INFO] DFAST_QC result json was written to GCA_018646345.1_ASM1864634v1_genomic.fna/dqc_result.json
[2023-06-18 14:35:31,094] [INFO] DFAST_QC completed!
[2023-06-18 14:35:31,094] [INFO] Total running time: 0h0m48s