[2023-06-28 16:34:15,790] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:34:15,791] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:34:15,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg185f9fc0-1c8e-4aee-8fe5-aadcd86fe702/dqc_reference
[2023-06-28 16:34:16,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:34:16,900] [INFO] Task started: Prodigal
[2023-06-28 16:34:16,900] [INFO] Running command: gunzip -c /var/lib/cwl/stgc04d08af-5d59-4ece-96be-b980369f830a/GCA_020025235.1_ASM2002523v1_genomic.fna.gz | prodigal -d GCA_020025235.1_ASM2002523v1_genomic.fna/cds.fna -a GCA_020025235.1_ASM2002523v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:34:22,104] [INFO] Task succeeded: Prodigal
[2023-06-28 16:34:22,104] [INFO] Task started: HMMsearch
[2023-06-28 16:34:22,104] [INFO] Running command: hmmsearch --tblout GCA_020025235.1_ASM2002523v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg185f9fc0-1c8e-4aee-8fe5-aadcd86fe702/dqc_reference/reference_markers.hmm GCA_020025235.1_ASM2002523v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:34:22,297] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:34:22,298] [INFO] Found 6/6 markers.
[2023-06-28 16:34:22,317] [INFO] Query marker FASTA was written to GCA_020025235.1_ASM2002523v1_genomic.fna/markers.fasta
[2023-06-28 16:34:22,317] [INFO] Task started: Blastn
[2023-06-28 16:34:22,317] [INFO] Running command: blastn -query GCA_020025235.1_ASM2002523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg185f9fc0-1c8e-4aee-8fe5-aadcd86fe702/dqc_reference/reference_markers.fasta -out GCA_020025235.1_ASM2002523v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:34:22,942] [INFO] Task succeeded: Blastn
[2023-06-28 16:34:22,945] [INFO] Selected 23 target genomes.
[2023-06-28 16:34:22,945] [INFO] Target genome list was writen to GCA_020025235.1_ASM2002523v1_genomic.fna/target_genomes.txt
[2023-06-28 16:34:22,947] [INFO] Task started: fastANI
[2023-06-28 16:34:22,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgc04d08af-5d59-4ece-96be-b980369f830a/GCA_020025235.1_ASM2002523v1_genomic.fna.gz --refList GCA_020025235.1_ASM2002523v1_genomic.fna/target_genomes.txt --output GCA_020025235.1_ASM2002523v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:34:36,096] [INFO] Task succeeded: fastANI
[2023-06-28 16:34:36,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg185f9fc0-1c8e-4aee-8fe5-aadcd86fe702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:34:36,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg185f9fc0-1c8e-4aee-8fe5-aadcd86fe702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:34:36,102] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:34:36,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:34:36,103] [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
Ruthenibacterium lactatiformans	strain=585-1	GCA_000949455.1	1550024	1550024	suspected-type	True	78.8587	241	627	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.7832	102	627	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	76.3469	64	627	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.1572	61	627	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:34:36,104] [INFO] DFAST Taxonomy check result was written to GCA_020025235.1_ASM2002523v1_genomic.fna/tc_result.tsv
[2023-06-28 16:34:36,105] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:34:36,105] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:34:36,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg185f9fc0-1c8e-4aee-8fe5-aadcd86fe702/dqc_reference/checkm_data
[2023-06-28 16:34:36,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:34:36,130] [INFO] Task started: CheckM
[2023-06-28 16:34:36,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025235.1_ASM2002523v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025235.1_ASM2002523v1_genomic.fna/checkm_input GCA_020025235.1_ASM2002523v1_genomic.fna/checkm_result
[2023-06-28 16:34:55,951] [INFO] Task succeeded: CheckM
[2023-06-28 16:34:55,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:34:55,969] [INFO] ===== Completeness check finished =====
[2023-06-28 16:34:55,970] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:34:55,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025235.1_ASM2002523v1_genomic.fna/markers.fasta)
[2023-06-28 16:34:55,971] [INFO] Task started: Blastn
[2023-06-28 16:34:55,971] [INFO] Running command: blastn -query GCA_020025235.1_ASM2002523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg185f9fc0-1c8e-4aee-8fe5-aadcd86fe702/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025235.1_ASM2002523v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:34:57,080] [INFO] Task succeeded: Blastn
[2023-06-28 16:34:57,083] [INFO] Selected 20 target genomes.
[2023-06-28 16:34:57,083] [INFO] Target genome list was writen to GCA_020025235.1_ASM2002523v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:34:57,093] [INFO] Task started: fastANI
[2023-06-28 16:34:57,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgc04d08af-5d59-4ece-96be-b980369f830a/GCA_020025235.1_ASM2002523v1_genomic.fna.gz --refList GCA_020025235.1_ASM2002523v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025235.1_ASM2002523v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:35:05,856] [INFO] Task succeeded: fastANI
[2023-06-28 16:35:05,865] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:35:05,865] [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_000949455.1	s__Ruthenibacterium lactatiformans	78.8587	241	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	98.75	98.24	0.81	0.72	47	-
GCA_014799685.1	s__Ruthenibacterium sp014799685	78.1052	173	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	97.75	97.75	0.71	0.71	2	-
GCA_910587145.1	s__Ruthenibacterium sp013316265	77.6692	175	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	99.81	99.81	0.95	0.95	2	-
GCA_019113785.1	s__Ruthenibacterium merdigallinarum	77.4438	136	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002315015.1	s__Ruthenibacterium avium	77.3296	91	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	98.44	98.37	0.86	0.85	3	-
GCA_018380115.1	s__Ruthenibacterium sp018380115	77.1457	107	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	97.78	95.38	0.91	0.83	6	-
GCF_002160145.1	s__Fournierella sp002160145	77.1006	86	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.11	98.11	0.91	0.91	2	-
GCA_905212515.1	s__Ruthenibacterium sp905212515	77.0477	115	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119935.1	s__Ruthenibacterium merdavium	76.7923	93	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	98.64	98.59	0.86	0.85	3	-
GCF_004345265.1	s__Fournierella massiliensis	76.7832	102	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.99	99.99	1.00	1.00	3	-
GCA_019119365.1	s__Gemmiger stercoripullorum	76.4628	70	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.12	98.12	0.82	0.82	2	-
GCF_014287275.1	s__Pygmaiobacter sp014287275	76.159	71	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pygmaiobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003343905.1	s__Gemmiger variabilis_C	76.0954	70	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483235.1	s__Faecalibacterium sp017483235	75.8084	52	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:35:05,867] [INFO] GTDB search result was written to GCA_020025235.1_ASM2002523v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:35:05,867] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:35:05,870] [INFO] DFAST_QC result json was written to GCA_020025235.1_ASM2002523v1_genomic.fna/dqc_result.json
[2023-06-28 16:35:05,871] [INFO] DFAST_QC completed!
[2023-06-28 16:35:05,871] [INFO] Total running time: 0h0m50s