[2023-06-08 07:23:41,817] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:23:41,820] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:23:41,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ae0e55b-fe88-4da8-8d24-6968ee4d0475/dqc_reference
[2023-06-08 07:23:43,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:23:43,176] [INFO] Task started: Prodigal
[2023-06-08 07:23:43,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c34196a-c9a2-439b-aff2-fbd63c616ed6/GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna.gz | prodigal -d GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/cds.fna -a GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:23:45,678] [INFO] Task succeeded: Prodigal
[2023-06-08 07:23:45,678] [INFO] Task started: HMMsearch
[2023-06-08 07:23:45,678] [INFO] Running command: hmmsearch --tblout GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ae0e55b-fe88-4da8-8d24-6968ee4d0475/dqc_reference/reference_markers.hmm GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:23:45,957] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:23:45,958] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c34196a-c9a2-439b-aff2-fbd63c616ed6/GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna.gz]
[2023-06-08 07:23:45,976] [INFO] Query marker FASTA was written to GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/markers.fasta
[2023-06-08 07:23:45,977] [INFO] Task started: Blastn
[2023-06-08 07:23:45,977] [INFO] Running command: blastn -query GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae0e55b-fe88-4da8-8d24-6968ee4d0475/dqc_reference/reference_markers.fasta -out GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:23:46,590] [INFO] Task succeeded: Blastn
[2023-06-08 07:23:46,604] [INFO] Selected 25 target genomes.
[2023-06-08 07:23:46,605] [INFO] Target genome list was writen to GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/target_genomes.txt
[2023-06-08 07:23:46,607] [INFO] Task started: fastANI
[2023-06-08 07:23:46,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c34196a-c9a2-439b-aff2-fbd63c616ed6/GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna.gz --refList GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/target_genomes.txt --output GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:23:59,165] [INFO] Task succeeded: fastANI
[2023-06-08 07:23:59,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ae0e55b-fe88-4da8-8d24-6968ee4d0475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:23:59,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ae0e55b-fe88-4da8-8d24-6968ee4d0475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:23:59,176] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:23:59,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:23:59,176] [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
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	75.1499	55	478	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	75.1341	67	478	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	75.1107	53	478	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	75.032	50	478	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	74.9721	55	478	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	74.9104	51	478	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	74.8943	66	478	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	74.8439	54	478	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	74.8148	70	478	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:23:59,178] [INFO] DFAST Taxonomy check result was written to GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/tc_result.tsv
[2023-06-08 07:23:59,179] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:23:59,179] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:23:59,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ae0e55b-fe88-4da8-8d24-6968ee4d0475/dqc_reference/checkm_data
[2023-06-08 07:23:59,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:23:59,209] [INFO] Task started: CheckM
[2023-06-08 07:23:59,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/checkm_input GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/checkm_result
[2023-06-08 07:24:15,574] [INFO] Task succeeded: CheckM
[2023-06-08 07:24:15,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 07:24:15,620] [INFO] ===== Completeness check finished =====
[2023-06-08 07:24:15,620] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:24:15,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/markers.fasta)
[2023-06-08 07:24:15,621] [INFO] Task started: Blastn
[2023-06-08 07:24:15,621] [INFO] Running command: blastn -query GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae0e55b-fe88-4da8-8d24-6968ee4d0475/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:16,398] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:16,403] [INFO] Selected 13 target genomes.
[2023-06-08 07:24:16,404] [INFO] Target genome list was writen to GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:24:16,405] [INFO] Task started: fastANI
[2023-06-08 07:24:16,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c34196a-c9a2-439b-aff2-fbd63c616ed6/GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna.gz --refList GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/target_genomes_gtdb.txt --output GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:24:20,405] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:20,422] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 07:24:20,423] [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_904387305.1	s__CAG-269 sp904387305	81.382	281	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419495.1	s__CAG-269 sp904419495	81.2722	283	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215845.1	s__CAG-269 sp905215845	81.1844	147	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553985.1	s__CAG-269 sp900553985	80.9929	262	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.48	98.04	0.82	0.80	5	-
GCA_000431335.1	s__CAG-269 sp000431335	80.202	244	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.17	98.64	0.90	0.86	6	-
GCA_905213875.1	s__CAG-269 sp905213875	80.0433	249	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.16	98.07	0.72	0.64	3	-
GCA_900556695.1	s__CAG-269 sp900556695	79.9373	166	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904384245.1	s__CAG-269 sp904384245	79.5215	216	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410505.1	s__CAG-269 sp017410505	79.4564	190	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904384205.1	s__CAG-269 sp904384205	79.3731	222	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438255.1	s__CAG-269 sp000438255	79.2068	191	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.47	98.35	0.85	0.83	3	-
GCA_900753165.1	s__CAG-269 sp900753165	79.0613	187	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.62	99.62	0.76	0.76	2	-
GCA_900554365.1	s__CAG-269 sp900554365	79.0372	211	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-08 07:24:20,425] [INFO] GTDB search result was written to GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/result_gtdb.tsv
[2023-06-08 07:24:20,425] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:24:20,430] [INFO] DFAST_QC result json was written to GCA_902461775.1_UHGG-TPA_MGYG-HGUT-00375_genomic.fna/dqc_result.json
[2023-06-08 07:24:20,430] [INFO] DFAST_QC completed!
[2023-06-08 07:24:20,430] [INFO] Total running time: 0h0m39s