[2023-06-30 00:13:26,293] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:13:26,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:13:26,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg4518e973-da46-4bdd-a9e8-b53afcc2832e/dqc_reference
[2023-06-30 00:13:27,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:13:27,576] [INFO] Task started: Prodigal
[2023-06-30 00:13:27,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg4162b4e2-2e14-4d97-9c09-a291563f1862/GCA_900751795.1_ERS235501_12_genomic.fna.gz | prodigal -d GCA_900751795.1_ERS235501_12_genomic.fna/cds.fna -a GCA_900751795.1_ERS235501_12_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:13:33,035] [INFO] Task succeeded: Prodigal
[2023-06-30 00:13:33,036] [INFO] Task started: HMMsearch
[2023-06-30 00:13:33,036] [INFO] Running command: hmmsearch --tblout GCA_900751795.1_ERS235501_12_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4518e973-da46-4bdd-a9e8-b53afcc2832e/dqc_reference/reference_markers.hmm GCA_900751795.1_ERS235501_12_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:13:33,247] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:13:33,248] [INFO] Found 6/6 markers.
[2023-06-30 00:13:33,274] [INFO] Query marker FASTA was written to GCA_900751795.1_ERS235501_12_genomic.fna/markers.fasta
[2023-06-30 00:13:33,274] [INFO] Task started: Blastn
[2023-06-30 00:13:33,274] [INFO] Running command: blastn -query GCA_900751795.1_ERS235501_12_genomic.fna/markers.fasta -db /var/lib/cwl/stg4518e973-da46-4bdd-a9e8-b53afcc2832e/dqc_reference/reference_markers.fasta -out GCA_900751795.1_ERS235501_12_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:13:33,961] [INFO] Task succeeded: Blastn
[2023-06-30 00:13:33,995] [INFO] Selected 8 target genomes.
[2023-06-30 00:13:33,996] [INFO] Target genome list was writen to GCA_900751795.1_ERS235501_12_genomic.fna/target_genomes.txt
[2023-06-30 00:13:33,997] [INFO] Task started: fastANI
[2023-06-30 00:13:33,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg4162b4e2-2e14-4d97-9c09-a291563f1862/GCA_900751795.1_ERS235501_12_genomic.fna.gz --refList GCA_900751795.1_ERS235501_12_genomic.fna/target_genomes.txt --output GCA_900751795.1_ERS235501_12_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:13:37,327] [INFO] Task succeeded: fastANI
[2023-06-30 00:13:37,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4518e973-da46-4bdd-a9e8-b53afcc2832e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:13:37,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4518e973-da46-4bdd-a9e8-b53afcc2832e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:13:37,335] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:13:37,335] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:13:37,336] [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	84.238	371	529	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	81.9051	290	529	95	below_threshold
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	81.6671	279	529	95	below_threshold
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	81.2558	251	529	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	81.1549	268	529	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.2002	182	529	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.1111	184	529	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.2675	156	529	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:13:37,338] [INFO] DFAST Taxonomy check result was written to GCA_900751795.1_ERS235501_12_genomic.fna/tc_result.tsv
[2023-06-30 00:13:37,338] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:13:37,339] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:13:37,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4518e973-da46-4bdd-a9e8-b53afcc2832e/dqc_reference/checkm_data
[2023-06-30 00:13:37,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:13:37,363] [INFO] Task started: CheckM
[2023-06-30 00:13:37,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900751795.1_ERS235501_12_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900751795.1_ERS235501_12_genomic.fna/checkm_input GCA_900751795.1_ERS235501_12_genomic.fna/checkm_result
[2023-06-30 00:14:00,216] [INFO] Task succeeded: CheckM
[2023-06-30 00:14:00,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:14:00,249] [INFO] ===== Completeness check finished =====
[2023-06-30 00:14:00,250] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:14:00,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900751795.1_ERS235501_12_genomic.fna/markers.fasta)
[2023-06-30 00:14:00,251] [INFO] Task started: Blastn
[2023-06-30 00:14:00,251] [INFO] Running command: blastn -query GCA_900751795.1_ERS235501_12_genomic.fna/markers.fasta -db /var/lib/cwl/stg4518e973-da46-4bdd-a9e8-b53afcc2832e/dqc_reference/reference_markers_gtdb.fasta -out GCA_900751795.1_ERS235501_12_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:14:01,473] [INFO] Task succeeded: Blastn
[2023-06-30 00:14:01,477] [INFO] Selected 11 target genomes.
[2023-06-30 00:14:01,477] [INFO] Target genome list was writen to GCA_900751795.1_ERS235501_12_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:14:01,479] [INFO] Task started: fastANI
[2023-06-30 00:14:01,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg4162b4e2-2e14-4d97-9c09-a291563f1862/GCA_900751795.1_ERS235501_12_genomic.fna.gz --refList GCA_900751795.1_ERS235501_12_genomic.fna/target_genomes_gtdb.txt --output GCA_900751795.1_ERS235501_12_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:14:06,545] [INFO] Task succeeded: fastANI
[2023-06-30 00:14:06,563] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:14:06,563] [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_905210055.1	s__Enorma sp900751795	99.7664	447	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	99.77	99.77	0.84	0.84	2	conclusive
GCA_900538305.1	s__Enorma sp900538305	94.1627	425	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333815.1	s__Enorma sp000333815	84.3408	355	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCF_902150035.1	s__Enorma burkinafasonensis	81.905	290	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000311845.1	s__Enorma massiliensis	81.6671	279	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	97.43	96.04	0.89	0.84	11	-
GCF_002159765.1	s__Coprousia sp002159765	80.2223	236	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	97.90	97.74	0.89	0.88	3	-
GCA_018715125.1	s__Coprousia avicola	80.0706	218	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161805.1	s__Coprousia sp002161805	80.0422	214	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901575.1	s__Limicola phocaeensis_A	79.8885	224	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160065.1	s__Limicola sp002160065	79.8559	213	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117005.1	s__Collinsella stercoripullorum	79.7411	218	529	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-30 00:14:06,565] [INFO] GTDB search result was written to GCA_900751795.1_ERS235501_12_genomic.fna/result_gtdb.tsv
[2023-06-30 00:14:06,566] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:14:06,571] [INFO] DFAST_QC result json was written to GCA_900751795.1_ERS235501_12_genomic.fna/dqc_result.json
[2023-06-30 00:14:06,571] [INFO] DFAST_QC completed!
[2023-06-30 00:14:06,572] [INFO] Total running time: 0h0m40s