[2023-06-28 01:45:54,100] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:45:54,112] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:45:54,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg32ffa8de-7434-44c1-9e37-e4c9279926a9/dqc_reference
[2023-06-28 01:45:55,372] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:45:55,374] [INFO] Task started: Prodigal
[2023-06-28 01:45:55,374] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0b3da89-6c78-425a-91e4-8bac5b07911f/GCA_944320245.1_E0_RM_bin158_genomic.fna.gz | prodigal -d GCA_944320245.1_E0_RM_bin158_genomic.fna/cds.fna -a GCA_944320245.1_E0_RM_bin158_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:46:02,511] [INFO] Task succeeded: Prodigal
[2023-06-28 01:46:02,511] [INFO] Task started: HMMsearch
[2023-06-28 01:46:02,511] [INFO] Running command: hmmsearch --tblout GCA_944320245.1_E0_RM_bin158_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32ffa8de-7434-44c1-9e37-e4c9279926a9/dqc_reference/reference_markers.hmm GCA_944320245.1_E0_RM_bin158_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:46:02,727] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:46:02,728] [INFO] Found 6/6 markers.
[2023-06-28 01:46:02,776] [INFO] Query marker FASTA was written to GCA_944320245.1_E0_RM_bin158_genomic.fna/markers.fasta
[2023-06-28 01:46:02,776] [INFO] Task started: Blastn
[2023-06-28 01:46:02,777] [INFO] Running command: blastn -query GCA_944320245.1_E0_RM_bin158_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ffa8de-7434-44c1-9e37-e4c9279926a9/dqc_reference/reference_markers.fasta -out GCA_944320245.1_E0_RM_bin158_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:46:03,546] [INFO] Task succeeded: Blastn
[2023-06-28 01:46:03,550] [INFO] Selected 12 target genomes.
[2023-06-28 01:46:03,550] [INFO] Target genome list was writen to GCA_944320245.1_E0_RM_bin158_genomic.fna/target_genomes.txt
[2023-06-28 01:46:03,561] [INFO] Task started: fastANI
[2023-06-28 01:46:03,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0b3da89-6c78-425a-91e4-8bac5b07911f/GCA_944320245.1_E0_RM_bin158_genomic.fna.gz --refList GCA_944320245.1_E0_RM_bin158_genomic.fna/target_genomes.txt --output GCA_944320245.1_E0_RM_bin158_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:46:09,408] [INFO] Task succeeded: fastANI
[2023-06-28 01:46:09,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32ffa8de-7434-44c1-9e37-e4c9279926a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:46:09,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32ffa8de-7434-44c1-9e37-e4c9279926a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:46:09,421] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 01:46:09,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 01:46:09,421] [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
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	97.2859	630	755	95	conclusive
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	83.9807	432	755	95	below_threshold
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	81.7981	376	755	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	81.6361	398	755	95	below_threshold
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	81.572	406	755	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.5526	295	755	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.2459	297	755	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.2186	304	755	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.9066	237	755	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.4077	273	755	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.5989	200	755	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	78.3483	196	755	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:46:09,424] [INFO] DFAST Taxonomy check result was written to GCA_944320245.1_E0_RM_bin158_genomic.fna/tc_result.tsv
[2023-06-28 01:46:09,425] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:46:09,425] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:46:09,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32ffa8de-7434-44c1-9e37-e4c9279926a9/dqc_reference/checkm_data
[2023-06-28 01:46:09,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:46:09,453] [INFO] Task started: CheckM
[2023-06-28 01:46:09,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320245.1_E0_RM_bin158_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320245.1_E0_RM_bin158_genomic.fna/checkm_input GCA_944320245.1_E0_RM_bin158_genomic.fna/checkm_result
[2023-06-28 01:46:35,522] [INFO] Task succeeded: CheckM
[2023-06-28 01:46:35,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:46:35,548] [INFO] ===== Completeness check finished =====
[2023-06-28 01:46:35,548] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:46:35,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320245.1_E0_RM_bin158_genomic.fna/markers.fasta)
[2023-06-28 01:46:35,549] [INFO] Task started: Blastn
[2023-06-28 01:46:35,549] [INFO] Running command: blastn -query GCA_944320245.1_E0_RM_bin158_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ffa8de-7434-44c1-9e37-e4c9279926a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320245.1_E0_RM_bin158_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:46:36,833] [INFO] Task succeeded: Blastn
[2023-06-28 01:46:36,837] [INFO] Selected 11 target genomes.
[2023-06-28 01:46:36,838] [INFO] Target genome list was writen to GCA_944320245.1_E0_RM_bin158_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:46:36,846] [INFO] Task started: fastANI
[2023-06-28 01:46:36,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0b3da89-6c78-425a-91e4-8bac5b07911f/GCA_944320245.1_E0_RM_bin158_genomic.fna.gz --refList GCA_944320245.1_E0_RM_bin158_genomic.fna/target_genomes_gtdb.txt --output GCA_944320245.1_E0_RM_bin158_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:46:42,415] [INFO] Task succeeded: fastANI
[2023-06-28 01:46:42,426] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:46:42,426] [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_000333815.1	s__Enorma sp000333815	97.117	625	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	conclusive
GCA_900538305.1	s__Enorma sp900538305	84.3143	468	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210055.1	s__Enorma sp900751795	84.2729	394	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	99.77	99.77	0.84	0.84	2	-
GCF_902150035.1	s__Enorma burkinafasonensis	84.0286	429	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186505.1	s__Enorma phocaeensis	81.7981	376	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117005.1	s__Collinsella stercoripullorum	81.7803	358	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_002159765.1	s__Coprousia sp002159765	81.6795	366	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	97.90	97.74	0.89	0.88	3	-
GCF_000311845.1	s__Enorma massiliensis	81.5602	407	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	97.43	96.04	0.89	0.84	11	-
GCA_018715125.1	s__Coprousia avicola	81.2106	346	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160065.1	s__Limicola sp002160065	80.8858	343	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014645.1	s__Collinsella sp008014645	79.6097	256	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-28 01:46:42,428] [INFO] GTDB search result was written to GCA_944320245.1_E0_RM_bin158_genomic.fna/result_gtdb.tsv
[2023-06-28 01:46:42,429] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:46:42,433] [INFO] DFAST_QC result json was written to GCA_944320245.1_E0_RM_bin158_genomic.fna/dqc_result.json
[2023-06-28 01:46:42,434] [INFO] DFAST_QC completed!
[2023-06-28 01:46:42,434] [INFO] Total running time: 0h0m48s