[2023-06-30 15:57:23,749] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:57:23,754] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:57:23,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg463bbe24-4f32-48cc-8929-4e4da98ed9f4/dqc_reference
[2023-06-30 15:57:26,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:57:26,139] [INFO] Task started: Prodigal
[2023-06-30 15:57:26,139] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ed4e68a-4ca7-4777-9ca1-6a688bc351c5/GCA_900757765.1_ERS537359_21_genomic.fna.gz | prodigal -d GCA_900757765.1_ERS537359_21_genomic.fna/cds.fna -a GCA_900757765.1_ERS537359_21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:57:30,625] [INFO] Task succeeded: Prodigal
[2023-06-30 15:57:30,625] [INFO] Task started: HMMsearch
[2023-06-30 15:57:30,625] [INFO] Running command: hmmsearch --tblout GCA_900757765.1_ERS537359_21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg463bbe24-4f32-48cc-8929-4e4da98ed9f4/dqc_reference/reference_markers.hmm GCA_900757765.1_ERS537359_21_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:57:30,857] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:57:30,859] [INFO] Found 6/6 markers.
[2023-06-30 15:57:30,887] [INFO] Query marker FASTA was written to GCA_900757765.1_ERS537359_21_genomic.fna/markers.fasta
[2023-06-30 15:57:30,888] [INFO] Task started: Blastn
[2023-06-30 15:57:30,888] [INFO] Running command: blastn -query GCA_900757765.1_ERS537359_21_genomic.fna/markers.fasta -db /var/lib/cwl/stg463bbe24-4f32-48cc-8929-4e4da98ed9f4/dqc_reference/reference_markers.fasta -out GCA_900757765.1_ERS537359_21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:57:31,466] [INFO] Task succeeded: Blastn
[2023-06-30 15:57:31,471] [INFO] Selected 17 target genomes.
[2023-06-30 15:57:31,471] [INFO] Target genome list was writen to GCA_900757765.1_ERS537359_21_genomic.fna/target_genomes.txt
[2023-06-30 15:57:31,473] [INFO] Task started: fastANI
[2023-06-30 15:57:31,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ed4e68a-4ca7-4777-9ca1-6a688bc351c5/GCA_900757765.1_ERS537359_21_genomic.fna.gz --refList GCA_900757765.1_ERS537359_21_genomic.fna/target_genomes.txt --output GCA_900757765.1_ERS537359_21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:57:39,497] [INFO] Task succeeded: fastANI
[2023-06-30 15:57:39,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg463bbe24-4f32-48cc-8929-4e4da98ed9f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:57:39,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg463bbe24-4f32-48cc-8929-4e4da98ed9f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:57:39,509] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 15:57:39,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 15:57:39,510] [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
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	99.0854	531	542	95	conclusive
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.3951	66	542	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.309	68	542	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.3059	69	542	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.6426	76	542	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.5887	63	542	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	76.4979	58	542	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:57:39,512] [INFO] DFAST Taxonomy check result was written to GCA_900757765.1_ERS537359_21_genomic.fna/tc_result.tsv
[2023-06-30 15:57:39,513] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:57:39,513] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:57:39,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg463bbe24-4f32-48cc-8929-4e4da98ed9f4/dqc_reference/checkm_data
[2023-06-30 15:57:39,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:57:39,536] [INFO] Task started: CheckM
[2023-06-30 15:57:39,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900757765.1_ERS537359_21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900757765.1_ERS537359_21_genomic.fna/checkm_input GCA_900757765.1_ERS537359_21_genomic.fna/checkm_result
[2023-06-30 15:58:00,093] [INFO] Task succeeded: CheckM
[2023-06-30 15:58:00,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:58:00,116] [INFO] ===== Completeness check finished =====
[2023-06-30 15:58:00,116] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:58:00,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900757765.1_ERS537359_21_genomic.fna/markers.fasta)
[2023-06-30 15:58:00,117] [INFO] Task started: Blastn
[2023-06-30 15:58:00,117] [INFO] Running command: blastn -query GCA_900757765.1_ERS537359_21_genomic.fna/markers.fasta -db /var/lib/cwl/stg463bbe24-4f32-48cc-8929-4e4da98ed9f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_900757765.1_ERS537359_21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:58:00,883] [INFO] Task succeeded: Blastn
[2023-06-30 15:58:00,889] [INFO] Selected 19 target genomes.
[2023-06-30 15:58:00,889] [INFO] Target genome list was writen to GCA_900757765.1_ERS537359_21_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:58:00,921] [INFO] Task started: fastANI
[2023-06-30 15:58:00,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ed4e68a-4ca7-4777-9ca1-6a688bc351c5/GCA_900757765.1_ERS537359_21_genomic.fna.gz --refList GCA_900757765.1_ERS537359_21_genomic.fna/target_genomes_gtdb.txt --output GCA_900757765.1_ERS537359_21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:58:09,638] [INFO] Task succeeded: fastANI
[2023-06-30 15:58:09,647] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:58:09,648] [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_003478275.1	s__AM51-8 sp003478275	99.0472	532	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	99.20	98.90	0.94	0.89	8	conclusive
GCA_900546435.1	s__AM51-8 sp900546435	82.4216	325	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	97.06	96.69	0.86	0.85	3	-
GCF_003479605.1	s__RUG115 sp900066395	77.376	61	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	98.27	97.78	0.88	0.83	29	-
GCA_900315735.1	s__RUG115 sp900315735	76.9146	57	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	99.35	98.93	0.92	0.85	5	-
GCF_014287635.1	s__1XD42-69 sp014287635	76.807	66	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.20	98.20	0.93	0.93	2	-
GCA_902363825.1	s__CAG-45 sp000438375	76.6765	67	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	98.60	98.28	0.92	0.87	6	-
GCF_000225345.1	s__Roseburia hominis	76.5887	63	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCF_003122485.1	s__Eubacterium_I ramulus_A	76.5003	55	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.76	98.61	0.82	0.80	7	-
GCA_900543445.1	s__Agathobacter sp900543445	76.301	53	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-30 15:58:09,650] [INFO] GTDB search result was written to GCA_900757765.1_ERS537359_21_genomic.fna/result_gtdb.tsv
[2023-06-30 15:58:09,651] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:58:09,654] [INFO] DFAST_QC result json was written to GCA_900757765.1_ERS537359_21_genomic.fna/dqc_result.json
[2023-06-30 15:58:09,654] [INFO] DFAST_QC completed!
[2023-06-30 15:58:09,654] [INFO] Total running time: 0h0m46s