[2023-06-05 15:05:44,578] [INFO] DFAST_QC pipeline started.
[2023-06-05 15:05:44,580] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 15:05:44,580] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf7143ca-045b-4a2b-9089-deb1ac5f06dd/dqc_reference
[2023-06-05 15:05:45,740] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 15:05:45,740] [INFO] Task started: Prodigal
[2023-06-05 15:05:45,741] [INFO] Running command: gunzip -c /var/lib/cwl/stge14a2534-93fc-4504-a6cf-5ed752a81058/GCA_934630905.1_ERR7738598_bin.362_genomic.fna.gz | prodigal -d GCA_934630905.1_ERR7738598_bin.362_genomic.fna/cds.fna -a GCA_934630905.1_ERR7738598_bin.362_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 15:05:51,575] [INFO] Task succeeded: Prodigal
[2023-06-05 15:05:51,575] [INFO] Task started: HMMsearch
[2023-06-05 15:05:51,575] [INFO] Running command: hmmsearch --tblout GCA_934630905.1_ERR7738598_bin.362_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf7143ca-045b-4a2b-9089-deb1ac5f06dd/dqc_reference/reference_markers.hmm GCA_934630905.1_ERR7738598_bin.362_genomic.fna/protein.faa > /dev/null
[2023-06-05 15:05:51,743] [INFO] Task succeeded: HMMsearch
[2023-06-05 15:05:51,744] [INFO] Found 6/6 markers.
[2023-06-05 15:05:51,764] [INFO] Query marker FASTA was written to GCA_934630905.1_ERR7738598_bin.362_genomic.fna/markers.fasta
[2023-06-05 15:05:51,764] [INFO] Task started: Blastn
[2023-06-05 15:05:51,764] [INFO] Running command: blastn -query GCA_934630905.1_ERR7738598_bin.362_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf7143ca-045b-4a2b-9089-deb1ac5f06dd/dqc_reference/reference_markers.fasta -out GCA_934630905.1_ERR7738598_bin.362_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:52,278] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:52,282] [INFO] Selected 17 target genomes.
[2023-06-05 15:05:52,282] [INFO] Target genome list was writen to GCA_934630905.1_ERR7738598_bin.362_genomic.fna/target_genomes.txt
[2023-06-05 15:05:52,286] [INFO] Task started: fastANI
[2023-06-05 15:05:52,286] [INFO] Running command: fastANI --query /var/lib/cwl/stge14a2534-93fc-4504-a6cf-5ed752a81058/GCA_934630905.1_ERR7738598_bin.362_genomic.fna.gz --refList GCA_934630905.1_ERR7738598_bin.362_genomic.fna/target_genomes.txt --output GCA_934630905.1_ERR7738598_bin.362_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 15:05:59,519] [INFO] Task succeeded: fastANI
[2023-06-05 15:05:59,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf7143ca-045b-4a2b-9089-deb1ac5f06dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 15:05:59,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf7143ca-045b-4a2b-9089-deb1ac5f06dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 15:05:59,526] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 15:05:59,526] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 15:05:59,526] [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
Senegalimassilia faecalis	strain=KGMB04484	GCA_004135645.1	2509433	2509433	type	True	76.7665	83	630	95	below_threshold
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	76.7327	59	630	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	76.6167	60	630	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	76.6104	60	630	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	76.6104	60	630	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	76.6016	59	630	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_017945865.1	2682776	2682776	type	True	76.4003	55	630	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_011392455.1	2682776	2682776	type	True	76.3733	56	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 15:05:59,527] [INFO] DFAST Taxonomy check result was written to GCA_934630905.1_ERR7738598_bin.362_genomic.fna/tc_result.tsv
[2023-06-05 15:05:59,528] [INFO] ===== Taxonomy check completed =====
[2023-06-05 15:05:59,528] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 15:05:59,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf7143ca-045b-4a2b-9089-deb1ac5f06dd/dqc_reference/checkm_data
[2023-06-05 15:05:59,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 15:05:59,566] [INFO] Task started: CheckM
[2023-06-05 15:05:59,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934630905.1_ERR7738598_bin.362_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934630905.1_ERR7738598_bin.362_genomic.fna/checkm_input GCA_934630905.1_ERR7738598_bin.362_genomic.fna/checkm_result
[2023-06-05 15:06:21,512] [INFO] Task succeeded: CheckM
[2023-06-05 15:06:21,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 15:06:21,531] [INFO] ===== Completeness check finished =====
[2023-06-05 15:06:21,532] [INFO] ===== Start GTDB Search =====
[2023-06-05 15:06:21,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934630905.1_ERR7738598_bin.362_genomic.fna/markers.fasta)
[2023-06-05 15:06:21,533] [INFO] Task started: Blastn
[2023-06-05 15:06:21,533] [INFO] Running command: blastn -query GCA_934630905.1_ERR7738598_bin.362_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf7143ca-045b-4a2b-9089-deb1ac5f06dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_934630905.1_ERR7738598_bin.362_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:06:22,257] [INFO] Task succeeded: Blastn
[2023-06-05 15:06:22,260] [INFO] Selected 24 target genomes.
[2023-06-05 15:06:22,260] [INFO] Target genome list was writen to GCA_934630905.1_ERR7738598_bin.362_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 15:06:22,404] [INFO] Task started: fastANI
[2023-06-05 15:06:22,404] [INFO] Running command: fastANI --query /var/lib/cwl/stge14a2534-93fc-4504-a6cf-5ed752a81058/GCA_934630905.1_ERR7738598_bin.362_genomic.fna.gz --refList GCA_934630905.1_ERR7738598_bin.362_genomic.fna/target_genomes_gtdb.txt --output GCA_934630905.1_ERR7738598_bin.362_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 15:06:31,245] [INFO] Task succeeded: fastANI
[2023-06-05 15:06:31,250] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 15:06:31,250] [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_017440565.1	s__RGIG3135 sp017440565	77.2601	66	630	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RGIG3135	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340345.1	s__Paraeggerthella hongkongensis_A	77.107	51	630	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella	95.0	98.75	98.26	0.95	0.89	5	-
GCF_000236865.1	s__Senegalimassilia anaerobia	76.7327	59	630	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.57	95.07	0.88	0.81	7	-
GCF_000024265.1	s__Eggerthella lenta	76.6167	60	630	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_011039175.1	s__D16-34 sp011039175	76.5639	51	630	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-34	95.0	98.08	98.08	0.92	0.92	2	-
GCA_017945865.1	s__D16-34 sp011392455	76.4003	55	630	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-34	95.0	97.96	96.85	0.90	0.86	4	-
--------------------------------------------------------------------------------
[2023-06-05 15:06:31,252] [INFO] GTDB search result was written to GCA_934630905.1_ERR7738598_bin.362_genomic.fna/result_gtdb.tsv
[2023-06-05 15:06:31,252] [INFO] ===== GTDB Search completed =====
[2023-06-05 15:06:31,255] [INFO] DFAST_QC result json was written to GCA_934630905.1_ERR7738598_bin.362_genomic.fna/dqc_result.json
[2023-06-05 15:06:31,255] [INFO] DFAST_QC completed!
[2023-06-05 15:06:31,255] [INFO] Total running time: 0h0m47s