[2023-06-08 03:14:23,217] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:23,221] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:23,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg70f66652-7ca3-4dc6-b48a-665a6ade76d6/dqc_reference
[2023-06-08 03:14:24,631] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:24,632] [INFO] Task started: Prodigal
[2023-06-08 03:14:24,632] [INFO] Running command: gunzip -c /var/lib/cwl/stgfac1ca3b-dd5f-4de4-bd15-8a69d0708da6/GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:32,408] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:32,408] [INFO] Task started: HMMsearch
[2023-06-08 03:14:32,409] [INFO] Running command: hmmsearch --tblout GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70f66652-7ca3-4dc6-b48a-665a6ade76d6/dqc_reference/reference_markers.hmm GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:32,688] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:32,690] [INFO] Found 6/6 markers.
[2023-06-08 03:14:32,727] [INFO] Query marker FASTA was written to GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:14:32,727] [INFO] Task started: Blastn
[2023-06-08 03:14:32,727] [INFO] Running command: blastn -query GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg70f66652-7ca3-4dc6-b48a-665a6ade76d6/dqc_reference/reference_markers.fasta -out GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:33,410] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:33,414] [INFO] Selected 27 target genomes.
[2023-06-08 03:14:33,415] [INFO] Target genome list was writen to GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:14:33,419] [INFO] Task started: fastANI
[2023-06-08 03:14:33,420] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac1ca3b-dd5f-4de4-bd15-8a69d0708da6/GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:47,347] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:47,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70f66652-7ca3-4dc6-b48a-665a6ade76d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:47,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70f66652-7ca3-4dc6-b48a-665a6ade76d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:47,350] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:14:47,350] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:14:47,350] [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
--------------------------------------------------------------------------------
[2023-06-08 03:14:47,353] [INFO] DFAST Taxonomy check result was written to GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:14:47,354] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:47,354] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:47,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70f66652-7ca3-4dc6-b48a-665a6ade76d6/dqc_reference/checkm_data
[2023-06-08 03:14:47,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:47,401] [INFO] Task started: CheckM
[2023-06-08 03:14:47,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:15:16,010] [INFO] Task succeeded: CheckM
[2023-06-08 03:15:16,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:15:16,030] [INFO] ===== Completeness check finished =====
[2023-06-08 03:15:16,031] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:15:16,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:15:16,031] [INFO] Task started: Blastn
[2023-06-08 03:15:16,032] [INFO] Running command: blastn -query GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg70f66652-7ca3-4dc6-b48a-665a6ade76d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:15:17,116] [INFO] Task succeeded: Blastn
[2023-06-08 03:15:17,120] [INFO] Selected 25 target genomes.
[2023-06-08 03:15:17,120] [INFO] Target genome list was writen to GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:15:17,126] [INFO] Task started: fastANI
[2023-06-08 03:15:17,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac1ca3b-dd5f-4de4-bd15-8a69d0708da6/GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:15:28,189] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:28,204] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:15:28,204] [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_902797075.1	s__UBA1066 sp902797075	98.1856	633	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902766945.1	s__UBA1066 sp902766945	77.9533	131	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002350625.1	s__UBA1066 sp002350625	77.9003	131	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.93	99.93	0.93	0.93	2	-
GCA_902773195.1	s__UBA1066 sp902773195	77.8141	170	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788035.1	s__UBA1066 sp902788035	77.5716	61	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.60	97.29	0.74	0.68	4	-
GCA_902773435.1	s__UBA1066 sp902773435	77.5284	176	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315305.1	s__UBA1066 sp900315305	77.2432	87	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	-
GCA_902766955.1	s__UBA1066 sp902766955	77.2361	132	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.96	97.96	0.75	0.75	2	-
GCA_900317515.1	s__UBA1066 sp900317515	76.9519	79	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.06	96.06	0.86	0.79	9	-
GCA_017514845.1	s__UBA1066 sp017514845	76.8976	56	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783935.1	s__UBA1066 sp902783935	76.8563	72	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320615.1	s__UBA1066 sp900320615	76.8025	52	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.42	99.12	0.88	0.79	4	-
GCA_015057835.1	s__UBA1066 sp015057835	76.5866	59	1055	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:15:28,206] [INFO] GTDB search result was written to GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:15:28,207] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:15:28,209] [INFO] DFAST_QC result json was written to GCA_947166475.1_SRR8387716_bin.96_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:15:28,210] [INFO] DFAST_QC completed!
[2023-06-08 03:15:28,210] [INFO] Total running time: 0h1m5s