[2023-06-13 10:10:44,025] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:44,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:44,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg541ba78d-7ad6-4bcb-8065-ace2406afe18/dqc_reference
[2023-06-13 10:10:45,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:10:45,269] [INFO] Task started: Prodigal
[2023-06-13 10:10:45,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b5ef78-b123-4ff8-a4e3-47cc312f74ee/GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:10:53,503] [INFO] Task succeeded: Prodigal
[2023-06-13 10:10:53,504] [INFO] Task started: HMMsearch
[2023-06-13 10:10:53,504] [INFO] Running command: hmmsearch --tblout GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg541ba78d-7ad6-4bcb-8065-ace2406afe18/dqc_reference/reference_markers.hmm GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:10:53,732] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:10:53,733] [INFO] Found 6/6 markers.
[2023-06-13 10:10:53,770] [INFO] Query marker FASTA was written to GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 10:10:53,770] [INFO] Task started: Blastn
[2023-06-13 10:10:53,770] [INFO] Running command: blastn -query GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg541ba78d-7ad6-4bcb-8065-ace2406afe18/dqc_reference/reference_markers.fasta -out GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:10:54,368] [INFO] Task succeeded: Blastn
[2023-06-13 10:10:54,378] [INFO] Selected 24 target genomes.
[2023-06-13 10:10:54,379] [INFO] Target genome list was writen to GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 10:10:54,381] [INFO] Task started: fastANI
[2023-06-13 10:10:54,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b5ef78-b123-4ff8-a4e3-47cc312f74ee/GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:06,777] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:06,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg541ba78d-7ad6-4bcb-8065-ace2406afe18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:06,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg541ba78d-7ad6-4bcb-8065-ace2406afe18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:06,781] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:06,781] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:11:06,781] [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
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	75.8796	69	1099	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:11:06,783] [INFO] DFAST Taxonomy check result was written to GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 10:11:06,783] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:06,783] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:06,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg541ba78d-7ad6-4bcb-8065-ace2406afe18/dqc_reference/checkm_data
[2023-06-13 10:11:06,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:06,822] [INFO] Task started: CheckM
[2023-06-13 10:11:06,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 10:11:35,972] [INFO] Task succeeded: CheckM
[2023-06-13 10:11:35,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:11:36,000] [INFO] ===== Completeness check finished =====
[2023-06-13 10:11:36,001] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:11:36,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 10:11:36,001] [INFO] Task started: Blastn
[2023-06-13 10:11:36,001] [INFO] Running command: blastn -query GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg541ba78d-7ad6-4bcb-8065-ace2406afe18/dqc_reference/reference_markers_gtdb.fasta -out GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:36,833] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:36,837] [INFO] Selected 13 target genomes.
[2023-06-13 10:11:36,837] [INFO] Target genome list was writen to GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:11:36,838] [INFO] Task started: fastANI
[2023-06-13 10:11:36,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b5ef78-b123-4ff8-a4e3-47cc312f74ee/GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:11:46,286] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:46,297] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:11:46,298] [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_910578345.1	s__UBA3282 sp009774575	96.963	884	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.18	99.18	0.92	0.92	2	conclusive
GCA_009774655.1	s__UBA3282 sp009774655	80.3243	431	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.36	98.36	0.78	0.78	2	-
GCA_910578115.1	s__UBA3282 sp910578115	80.1746	528	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588215.1	s__UBA3282 sp910588215	79.9643	503	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575245.1	s__UBA3282 sp910575245	79.5671	515	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.49	99.49	0.95	0.95	2	-
GCA_910578555.1	s__UBA3282 sp910578555	78.1506	318	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586615.1	s__UBA3282 sp910586615	78.0539	323	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804355.1	s__UBA3282 sp014804355	77.8334	286	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612405.1	s__UBA3282 sp003612405	77.6026	233	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.19	99.19	0.85	0.85	2	-
GCA_002492525.1	s__UBA3282 sp002492525	77.38	186	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.83	99.82	0.86	0.82	3	-
GCA_003611805.1	s__UBA3282 sp003611805	77.2709	195	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.73	98.68	0.87	0.86	4	-
GCA_002493835.1	s__UBA3282 sp002493835	77.2448	141	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579505.1	s__UBA3282 sp910579505	77.12	202	1099	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:11:46,299] [INFO] GTDB search result was written to GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 10:11:46,300] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:11:46,302] [INFO] DFAST_QC result json was written to GCA_947063835.1_SRR12358625_bin.32_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 10:11:46,303] [INFO] DFAST_QC completed!
[2023-06-13 10:11:46,303] [INFO] Total running time: 0h1m2s