[2023-06-04 22:42:04,591] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:42:04,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:42:04,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgb87a4797-998a-4c21-9276-963f2426d7fe/dqc_reference
[2023-06-04 22:42:06,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:42:06,888] [INFO] Task started: Prodigal
[2023-06-04 22:42:06,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg410f7012-4196-433e-88cf-9c171a6c9010/GCA_902836295.1_MGYG-HGUT-04975_genomic.fna.gz | prodigal -d GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/cds.fna -a GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:42:09,317] [INFO] Task succeeded: Prodigal
[2023-06-04 22:42:09,318] [INFO] Task started: HMMsearch
[2023-06-04 22:42:09,318] [INFO] Running command: hmmsearch --tblout GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb87a4797-998a-4c21-9276-963f2426d7fe/dqc_reference/reference_markers.hmm GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:42:09,516] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:42:09,518] [INFO] Found 6/6 markers.
[2023-06-04 22:42:09,539] [INFO] Query marker FASTA was written to GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/markers.fasta
[2023-06-04 22:42:09,540] [INFO] Task started: Blastn
[2023-06-04 22:42:09,540] [INFO] Running command: blastn -query GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87a4797-998a-4c21-9276-963f2426d7fe/dqc_reference/reference_markers.fasta -out GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:42:11,108] [INFO] Task succeeded: Blastn
[2023-06-04 22:42:11,112] [INFO] Selected 12 target genomes.
[2023-06-04 22:42:11,113] [INFO] Target genome list was writen to GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/target_genomes.txt
[2023-06-04 22:42:11,115] [INFO] Task started: fastANI
[2023-06-04 22:42:11,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg410f7012-4196-433e-88cf-9c171a6c9010/GCA_902836295.1_MGYG-HGUT-04975_genomic.fna.gz --refList GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/target_genomes.txt --output GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:42:14,803] [INFO] Task succeeded: fastANI
[2023-06-04 22:42:14,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb87a4797-998a-4c21-9276-963f2426d7fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:42:14,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb87a4797-998a-4c21-9276-963f2426d7fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:42:14,817] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:42:14,817] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 22:42:14,817] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	84.8856	124	148	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	84.5338	115	148	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	81.1887	91	148	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.2735	73	148	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.7375	52	148	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.6845	52	148	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.6382	68	148	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.4629	60	148	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.049	50	148	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.5268	60	148	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:42:14,819] [INFO] DFAST Taxonomy check result was written to GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/tc_result.tsv
[2023-06-04 22:42:14,820] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:42:14,820] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:42:14,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb87a4797-998a-4c21-9276-963f2426d7fe/dqc_reference/checkm_data
[2023-06-04 22:42:14,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:42:14,836] [INFO] Task started: CheckM
[2023-06-04 22:42:14,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/checkm_input GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/checkm_result
[2023-06-04 22:42:29,571] [INFO] Task succeeded: CheckM
[2023-06-04 22:42:29,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:42:29,592] [INFO] ===== Completeness check finished =====
[2023-06-04 22:42:29,592] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:42:29,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/markers.fasta)
[2023-06-04 22:42:29,593] [INFO] Task started: Blastn
[2023-06-04 22:42:29,593] [INFO] Running command: blastn -query GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87a4797-998a-4c21-9276-963f2426d7fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:42:31,012] [INFO] Task succeeded: Blastn
[2023-06-04 22:42:31,016] [INFO] Selected 13 target genomes.
[2023-06-04 22:42:31,016] [INFO] Target genome list was writen to GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:42:31,047] [INFO] Task started: fastANI
[2023-06-04 22:42:31,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg410f7012-4196-433e-88cf-9c171a6c9010/GCA_902836295.1_MGYG-HGUT-04975_genomic.fna.gz --refList GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/target_genomes_gtdb.txt --output GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:42:35,342] [INFO] Task succeeded: fastANI
[2023-06-04 22:42:35,358] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:42:35,358] [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
GCF_014982725.1	s__Thermophilibacter sp014982725	96.9948	132	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002159735.1	s__Thermophilibacter sp002159735	88.8773	126	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899935.1	s__Thermophilibacter uli_B	87.7717	122	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116265.1	s__Thermophilibacter stercoravium	87.4738	113	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305805.1	s__Thermophilibacter excrementavium	87.3798	124	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.86	97.86	0.86	0.86	2	-
GCF_900119915.1	s__Thermophilibacter timonensis	87.2734	119	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	98.93	98.03	0.94	0.92	4	-
GCF_012027725.1	s__Thermophilibacter sp012027725	86.0305	122	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900775.1	s__Thermophilibacter uli_A	85.8079	123	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	85.3291	116	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128445.1	s__Thermophilibacter provencensis	84.8856	124	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	96.98	96.17	0.87	0.80	3	-
GCF_002159625.1	s__Thermophilibacter avicola	84.8647	116	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCF_002160255.1	s__Thermophilibacter avistercoris	84.7264	118	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.79	97.22	0.93	0.92	5	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	84.4468	116	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 22:42:35,360] [INFO] GTDB search result was written to GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/result_gtdb.tsv
[2023-06-04 22:42:35,361] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:42:35,364] [INFO] DFAST_QC result json was written to GCA_902836295.1_MGYG-HGUT-04975_genomic.fna/dqc_result.json
[2023-06-04 22:42:35,364] [INFO] DFAST_QC completed!
[2023-06-04 22:42:35,364] [INFO] Total running time: 0h0m31s