[2023-07-01 03:51:16,491] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:51:16,493] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:51:16,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg129fd92c-6927-4156-b914-87a54e73c8ce/dqc_reference
[2023-07-01 03:51:17,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:51:17,720] [INFO] Task started: Prodigal
[2023-07-01 03:51:17,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg271df24d-f7a4-4e37-8a16-625fe8551205/GCA_016290665.1_ASM1629066v1_genomic.fna.gz | prodigal -d GCA_016290665.1_ASM1629066v1_genomic.fna/cds.fna -a GCA_016290665.1_ASM1629066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:51:23,643] [INFO] Task succeeded: Prodigal
[2023-07-01 03:51:23,644] [INFO] Task started: HMMsearch
[2023-07-01 03:51:23,644] [INFO] Running command: hmmsearch --tblout GCA_016290665.1_ASM1629066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg129fd92c-6927-4156-b914-87a54e73c8ce/dqc_reference/reference_markers.hmm GCA_016290665.1_ASM1629066v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:51:23,866] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:51:23,868] [INFO] Found 6/6 markers.
[2023-07-01 03:51:23,893] [INFO] Query marker FASTA was written to GCA_016290665.1_ASM1629066v1_genomic.fna/markers.fasta
[2023-07-01 03:51:23,894] [INFO] Task started: Blastn
[2023-07-01 03:51:23,894] [INFO] Running command: blastn -query GCA_016290665.1_ASM1629066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg129fd92c-6927-4156-b914-87a54e73c8ce/dqc_reference/reference_markers.fasta -out GCA_016290665.1_ASM1629066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:51:24,603] [INFO] Task succeeded: Blastn
[2023-07-01 03:51:24,611] [INFO] Selected 27 target genomes.
[2023-07-01 03:51:24,612] [INFO] Target genome list was writen to GCA_016290665.1_ASM1629066v1_genomic.fna/target_genomes.txt
[2023-07-01 03:51:24,613] [INFO] Task started: fastANI
[2023-07-01 03:51:24,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg271df24d-f7a4-4e37-8a16-625fe8551205/GCA_016290665.1_ASM1629066v1_genomic.fna.gz --refList GCA_016290665.1_ASM1629066v1_genomic.fna/target_genomes.txt --output GCA_016290665.1_ASM1629066v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:51:40,069] [INFO] Task succeeded: fastANI
[2023-07-01 03:51:40,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg129fd92c-6927-4156-b914-87a54e73c8ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:51:40,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg129fd92c-6927-4156-b914-87a54e73c8ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:51:40,077] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:51:40,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:51:40,077] [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
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.8659	58	696	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.5249	51	696	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.0911	51	696	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:51:40,079] [INFO] DFAST Taxonomy check result was written to GCA_016290665.1_ASM1629066v1_genomic.fna/tc_result.tsv
[2023-07-01 03:51:40,080] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:51:40,080] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:51:40,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg129fd92c-6927-4156-b914-87a54e73c8ce/dqc_reference/checkm_data
[2023-07-01 03:51:40,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:51:40,111] [INFO] Task started: CheckM
[2023-07-01 03:51:40,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016290665.1_ASM1629066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016290665.1_ASM1629066v1_genomic.fna/checkm_input GCA_016290665.1_ASM1629066v1_genomic.fna/checkm_result
[2023-07-01 03:52:03,707] [INFO] Task succeeded: CheckM
[2023-07-01 03:52:03,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:52:03,731] [INFO] ===== Completeness check finished =====
[2023-07-01 03:52:03,731] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:52:03,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016290665.1_ASM1629066v1_genomic.fna/markers.fasta)
[2023-07-01 03:52:03,732] [INFO] Task started: Blastn
[2023-07-01 03:52:03,733] [INFO] Running command: blastn -query GCA_016290665.1_ASM1629066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg129fd92c-6927-4156-b914-87a54e73c8ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_016290665.1_ASM1629066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:52:04,977] [INFO] Task succeeded: Blastn
[2023-07-01 03:52:04,981] [INFO] Selected 12 target genomes.
[2023-07-01 03:52:04,982] [INFO] Target genome list was writen to GCA_016290665.1_ASM1629066v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:52:05,017] [INFO] Task started: fastANI
[2023-07-01 03:52:05,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg271df24d-f7a4-4e37-8a16-625fe8551205/GCA_016290665.1_ASM1629066v1_genomic.fna.gz --refList GCA_016290665.1_ASM1629066v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016290665.1_ASM1629066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:52:10,728] [INFO] Task succeeded: fastANI
[2023-07-01 03:52:10,741] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:52:10,741] [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_016290665.1	s__UBA6857 sp016290665	100.0	687	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017544665.1	s__UBA6857 sp017544665	83.6763	451	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786285.1	s__UBA6857 sp902786285	82.4602	459	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	96.81	96.53	0.83	0.83	3	-
GCA_902761265.1	s__UBA6857 sp902761265	81.7387	392	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774035.1	s__UBA6857 sp902774035	80.7239	326	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434855.1	s__UBA6857 sp017434855	80.467	359	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	98.64	98.64	0.90	0.90	2	-
GCA_017454485.1	s__UBA6857 sp017454485	79.8608	304	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792985.1	s__UBA6857 sp902792985	79.6554	308	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902772935.1	s__UBA6857 sp902772935	79.1429	275	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430145.1	s__RUG806 sp017430145	77.3054	118	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG806	95.0	98.10	97.98	0.82	0.79	3	-
GCA_902796315.1	s__DTU089 sp902796315	76.717	79	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 03:52:10,743] [INFO] GTDB search result was written to GCA_016290665.1_ASM1629066v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:52:10,744] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:52:10,748] [INFO] DFAST_QC result json was written to GCA_016290665.1_ASM1629066v1_genomic.fna/dqc_result.json
[2023-07-01 03:52:10,748] [INFO] DFAST_QC completed!
[2023-07-01 03:52:10,749] [INFO] Total running time: 0h0m54s