[2023-06-29 22:34:27,458] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:34:27,461] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:34:27,461] [INFO] DQC Reference Directory: /var/lib/cwl/stga0c3a265-5503-4612-886b-8191e57fd0d6/dqc_reference
[2023-06-29 22:34:28,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:34:28,707] [INFO] Task started: Prodigal
[2023-06-29 22:34:28,707] [INFO] Running command: gunzip -c /var/lib/cwl/stgceddcfad-f3fa-4216-9432-9c5669497e70/GCA_900758175.1_ERS608493_23_genomic.fna.gz | prodigal -d GCA_900758175.1_ERS608493_23_genomic.fna/cds.fna -a GCA_900758175.1_ERS608493_23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:34:36,390] [INFO] Task succeeded: Prodigal
[2023-06-29 22:34:36,391] [INFO] Task started: HMMsearch
[2023-06-29 22:34:36,391] [INFO] Running command: hmmsearch --tblout GCA_900758175.1_ERS608493_23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0c3a265-5503-4612-886b-8191e57fd0d6/dqc_reference/reference_markers.hmm GCA_900758175.1_ERS608493_23_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:34:36,638] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:34:36,640] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgceddcfad-f3fa-4216-9432-9c5669497e70/GCA_900758175.1_ERS608493_23_genomic.fna.gz]
[2023-06-29 22:34:36,672] [INFO] Query marker FASTA was written to GCA_900758175.1_ERS608493_23_genomic.fna/markers.fasta
[2023-06-29 22:34:36,672] [INFO] Task started: Blastn
[2023-06-29 22:34:36,672] [INFO] Running command: blastn -query GCA_900758175.1_ERS608493_23_genomic.fna/markers.fasta -db /var/lib/cwl/stga0c3a265-5503-4612-886b-8191e57fd0d6/dqc_reference/reference_markers.fasta -out GCA_900758175.1_ERS608493_23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:34:37,270] [INFO] Task succeeded: Blastn
[2023-06-29 22:34:37,274] [INFO] Selected 25 target genomes.
[2023-06-29 22:34:37,275] [INFO] Target genome list was writen to GCA_900758175.1_ERS608493_23_genomic.fna/target_genomes.txt
[2023-06-29 22:34:37,283] [INFO] Task started: fastANI
[2023-06-29 22:34:37,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgceddcfad-f3fa-4216-9432-9c5669497e70/GCA_900758175.1_ERS608493_23_genomic.fna.gz --refList GCA_900758175.1_ERS608493_23_genomic.fna/target_genomes.txt --output GCA_900758175.1_ERS608493_23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:34:54,992] [INFO] Task succeeded: fastANI
[2023-06-29 22:34:54,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0c3a265-5503-4612-886b-8191e57fd0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:34:54,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0c3a265-5503-4612-886b-8191e57fd0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:34:54,998] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:34:54,999] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:34:54,999] [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
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	74.7005	63	911	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	74.6587	66	911	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	74.6273	60	911	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:34:55,001] [INFO] DFAST Taxonomy check result was written to GCA_900758175.1_ERS608493_23_genomic.fna/tc_result.tsv
[2023-06-29 22:34:55,002] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:34:55,002] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:34:55,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0c3a265-5503-4612-886b-8191e57fd0d6/dqc_reference/checkm_data
[2023-06-29 22:34:55,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:34:55,039] [INFO] Task started: CheckM
[2023-06-29 22:34:55,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900758175.1_ERS608493_23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900758175.1_ERS608493_23_genomic.fna/checkm_input GCA_900758175.1_ERS608493_23_genomic.fna/checkm_result
[2023-06-29 22:35:23,499] [INFO] Task succeeded: CheckM
[2023-06-29 22:35:23,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:35:23,522] [INFO] ===== Completeness check finished =====
[2023-06-29 22:35:23,522] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:35:23,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900758175.1_ERS608493_23_genomic.fna/markers.fasta)
[2023-06-29 22:35:23,523] [INFO] Task started: Blastn
[2023-06-29 22:35:23,523] [INFO] Running command: blastn -query GCA_900758175.1_ERS608493_23_genomic.fna/markers.fasta -db /var/lib/cwl/stga0c3a265-5503-4612-886b-8191e57fd0d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_900758175.1_ERS608493_23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:35:24,405] [INFO] Task succeeded: Blastn
[2023-06-29 22:35:24,410] [INFO] Selected 18 target genomes.
[2023-06-29 22:35:24,410] [INFO] Target genome list was writen to GCA_900758175.1_ERS608493_23_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:35:24,457] [INFO] Task started: fastANI
[2023-06-29 22:35:24,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgceddcfad-f3fa-4216-9432-9c5669497e70/GCA_900758175.1_ERS608493_23_genomic.fna.gz --refList GCA_900758175.1_ERS608493_23_genomic.fna/target_genomes_gtdb.txt --output GCA_900758175.1_ERS608493_23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:35:34,435] [INFO] Task succeeded: fastANI
[2023-06-29 22:35:34,456] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:35:34,456] [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_004556395.1	s__SFHK01 sp004556395	98.8079	821	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	99.09	98.81	0.92	0.90	3	conclusive
GCA_017522345.1	s__SFHK01 sp017522345	78.2781	193	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555155.1	s__Faecivicinus sp004555155	78.2227	146	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017552535.1	s__RUG14130 sp017552535	78.1432	164	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG14130	95.0	97.52	97.52	0.84	0.84	2	-
GCA_015056255.1	s__SFHK01 sp015056255	77.9667	188	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017396845.1	s__SFHK01 sp017396845	77.8728	205	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777335.1	s__UBA2862 sp902777335	77.8625	173	911	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_902796025.1	s__RUG14130 sp902796025	77.7851	154	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG14130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296675.1	s__SFHK01 sp016296675	77.7664	154	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	96.60	96.60	0.77	0.77	2	-
GCA_018716805.1	s__Faecivicinus avistercoris	77.7591	158	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecivicinus	95.0	96.88	96.88	0.84	0.84	2	-
GCA_017543905.1	s__RUG14130 sp017543905	77.6254	140	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG14130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799465.1	s__UBA2862 sp902799465	77.5193	149	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	97.80	97.80	0.88	0.88	2	-
GCA_017480045.1	s__UBA2862 sp017480045	77.2641	129	911	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_902778045.1	s__UBA2862 sp902778045	77.0802	117	911	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_017434085.1	s__UBA2862 sp017434085	76.7498	112	911	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_017412445.1	s__RUG14130 sp017412445	76.7014	101	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG14130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514855.1	s__Pullichristensenella sp012514855	76.184	85	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Pullichristensenella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:35:34,481] [INFO] GTDB search result was written to GCA_900758175.1_ERS608493_23_genomic.fna/result_gtdb.tsv
[2023-06-29 22:35:34,482] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:35:34,487] [INFO] DFAST_QC result json was written to GCA_900758175.1_ERS608493_23_genomic.fna/dqc_result.json
[2023-06-29 22:35:34,488] [INFO] DFAST_QC completed!
[2023-06-29 22:35:34,488] [INFO] Total running time: 0h1m7s