[2023-06-05 03:09:43,526] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:09:43,530] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:09:43,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg95ecf3b7-1127-4dba-97ae-b0ba45cc162e/dqc_reference
[2023-06-05 03:09:45,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:09:45,442] [INFO] Task started: Prodigal
[2023-06-05 03:09:45,442] [INFO] Running command: gunzip -c /var/lib/cwl/stg71dae5bb-1fe9-4876-9050-1f0d37ea3edd/GCA_004563405.1_ASM456340v1_genomic.fna.gz | prodigal -d GCA_004563405.1_ASM456340v1_genomic.fna/cds.fna -a GCA_004563405.1_ASM456340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:09:53,351] [INFO] Task succeeded: Prodigal
[2023-06-05 03:09:53,352] [INFO] Task started: HMMsearch
[2023-06-05 03:09:53,352] [INFO] Running command: hmmsearch --tblout GCA_004563405.1_ASM456340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95ecf3b7-1127-4dba-97ae-b0ba45cc162e/dqc_reference/reference_markers.hmm GCA_004563405.1_ASM456340v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:09:53,699] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:09:53,701] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg71dae5bb-1fe9-4876-9050-1f0d37ea3edd/GCA_004563405.1_ASM456340v1_genomic.fna.gz]
[2023-06-05 03:09:53,731] [INFO] Query marker FASTA was written to GCA_004563405.1_ASM456340v1_genomic.fna/markers.fasta
[2023-06-05 03:09:53,732] [INFO] Task started: Blastn
[2023-06-05 03:09:53,732] [INFO] Running command: blastn -query GCA_004563405.1_ASM456340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ecf3b7-1127-4dba-97ae-b0ba45cc162e/dqc_reference/reference_markers.fasta -out GCA_004563405.1_ASM456340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:09:54,469] [INFO] Task succeeded: Blastn
[2023-06-05 03:09:54,473] [INFO] Selected 28 target genomes.
[2023-06-05 03:09:54,474] [INFO] Target genome list was writen to GCA_004563405.1_ASM456340v1_genomic.fna/target_genomes.txt
[2023-06-05 03:09:54,479] [INFO] Task started: fastANI
[2023-06-05 03:09:54,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg71dae5bb-1fe9-4876-9050-1f0d37ea3edd/GCA_004563405.1_ASM456340v1_genomic.fna.gz --refList GCA_004563405.1_ASM456340v1_genomic.fna/target_genomes.txt --output GCA_004563405.1_ASM456340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:10:08,635] [INFO] Task succeeded: fastANI
[2023-06-05 03:10:08,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95ecf3b7-1127-4dba-97ae-b0ba45cc162e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:10:08,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95ecf3b7-1127-4dba-97ae-b0ba45cc162e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:10:08,652] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:10:08,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:10:08,652] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.4469	68	854	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.2539	64	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:10:08,655] [INFO] DFAST Taxonomy check result was written to GCA_004563405.1_ASM456340v1_genomic.fna/tc_result.tsv
[2023-06-05 03:10:08,656] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:10:08,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:10:08,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95ecf3b7-1127-4dba-97ae-b0ba45cc162e/dqc_reference/checkm_data
[2023-06-05 03:10:08,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:10:08,697] [INFO] Task started: CheckM
[2023-06-05 03:10:08,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004563405.1_ASM456340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004563405.1_ASM456340v1_genomic.fna/checkm_input GCA_004563405.1_ASM456340v1_genomic.fna/checkm_result
[2023-06-05 03:10:37,436] [INFO] Task succeeded: CheckM
[2023-06-05 03:10:37,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 6.02%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-05 03:10:37,461] [INFO] ===== Completeness check finished =====
[2023-06-05 03:10:37,461] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:10:37,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004563405.1_ASM456340v1_genomic.fna/markers.fasta)
[2023-06-05 03:10:37,462] [INFO] Task started: Blastn
[2023-06-05 03:10:37,462] [INFO] Running command: blastn -query GCA_004563405.1_ASM456340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ecf3b7-1127-4dba-97ae-b0ba45cc162e/dqc_reference/reference_markers_gtdb.fasta -out GCA_004563405.1_ASM456340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:10:38,682] [INFO] Task succeeded: Blastn
[2023-06-05 03:10:38,685] [INFO] Selected 12 target genomes.
[2023-06-05 03:10:38,685] [INFO] Target genome list was writen to GCA_004563405.1_ASM456340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:10:38,689] [INFO] Task started: fastANI
[2023-06-05 03:10:38,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg71dae5bb-1fe9-4876-9050-1f0d37ea3edd/GCA_004563405.1_ASM456340v1_genomic.fna.gz --refList GCA_004563405.1_ASM456340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004563405.1_ASM456340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:10:46,488] [INFO] Task succeeded: fastANI
[2023-06-05 03:10:46,510] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:10:46,510] [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_004563405.1	s__SFTH01 sp004563405	100.0	852	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004557125.1	s__SFTH01 sp004557125	84.625	528	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554085.1	s__SFTH01 sp004554085	84.5058	532	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938785.1	s__SFTH01 sp017938785	80.6803	327	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317565.1	s__UBA2862 sp900317565	80.4072	318	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	99.55	99.55	0.85	0.85	2	-
GCA_017481065.1	s__SFTH01 sp017481065	80.3073	364	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765395.1	s__UBA2862 sp902765395	80.2145	299	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553265.1	s__Faecivicinus sp900553265	80.0511	300	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecivicinus	95.0	98.26	98.26	0.81	0.81	2	-
GCA_902790525.1	s__UBA2862 sp902790525	80.0492	322	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315585.1	s__UBA2862 sp900315585	80.0312	299	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.00	97.28	0.87	0.83	5	-
GCA_902799045.1	s__UBA2862 sp902799045	79.8371	272	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790175.1	s__UBA2862 sp902790175	79.6453	268	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 03:10:46,513] [INFO] GTDB search result was written to GCA_004563405.1_ASM456340v1_genomic.fna/result_gtdb.tsv
[2023-06-05 03:10:46,513] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:10:46,517] [INFO] DFAST_QC result json was written to GCA_004563405.1_ASM456340v1_genomic.fna/dqc_result.json
[2023-06-05 03:10:46,517] [INFO] DFAST_QC completed!
[2023-06-05 03:10:46,517] [INFO] Total running time: 0h1m3s