[2023-06-29 09:02:33,104] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:33,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:33,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg17ba8b27-ad10-4eaf-9e70-e00795f5abc9/dqc_reference
[2023-06-29 09:02:34,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:34,506] [INFO] Task started: Prodigal
[2023-06-29 09:02:34,507] [INFO] Running command: gunzip -c /var/lib/cwl/stg966fb3d2-f08a-4a4f-92de-38fdd0b37539/GCA_020859995.1_ASM2085999v1_genomic.fna.gz | prodigal -d GCA_020859995.1_ASM2085999v1_genomic.fna/cds.fna -a GCA_020859995.1_ASM2085999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:44,758] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:44,758] [INFO] Task started: HMMsearch
[2023-06-29 09:02:44,759] [INFO] Running command: hmmsearch --tblout GCA_020859995.1_ASM2085999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17ba8b27-ad10-4eaf-9e70-e00795f5abc9/dqc_reference/reference_markers.hmm GCA_020859995.1_ASM2085999v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:45,059] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:45,060] [INFO] Found 6/6 markers.
[2023-06-29 09:02:45,099] [INFO] Query marker FASTA was written to GCA_020859995.1_ASM2085999v1_genomic.fna/markers.fasta
[2023-06-29 09:02:45,099] [INFO] Task started: Blastn
[2023-06-29 09:02:45,099] [INFO] Running command: blastn -query GCA_020859995.1_ASM2085999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17ba8b27-ad10-4eaf-9e70-e00795f5abc9/dqc_reference/reference_markers.fasta -out GCA_020859995.1_ASM2085999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:45,775] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:45,779] [INFO] Selected 32 target genomes.
[2023-06-29 09:02:45,779] [INFO] Target genome list was writen to GCA_020859995.1_ASM2085999v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:45,783] [INFO] Task started: fastANI
[2023-06-29 09:02:45,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg966fb3d2-f08a-4a4f-92de-38fdd0b37539/GCA_020859995.1_ASM2085999v1_genomic.fna.gz --refList GCA_020859995.1_ASM2085999v1_genomic.fna/target_genomes.txt --output GCA_020859995.1_ASM2085999v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:03:05,586] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:05,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17ba8b27-ad10-4eaf-9e70-e00795f5abc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:03:05,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17ba8b27-ad10-4eaf-9e70-e00795f5abc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:03:05,595] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:03:05,596] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:03:05,596] [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
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.0289	53	1350	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	75.7588	52	1350	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:03:05,598] [INFO] DFAST Taxonomy check result was written to GCA_020859995.1_ASM2085999v1_genomic.fna/tc_result.tsv
[2023-06-29 09:03:05,599] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:03:05,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:03:05,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17ba8b27-ad10-4eaf-9e70-e00795f5abc9/dqc_reference/checkm_data
[2023-06-29 09:03:05,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:03:05,672] [INFO] Task started: CheckM
[2023-06-29 09:03:05,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020859995.1_ASM2085999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020859995.1_ASM2085999v1_genomic.fna/checkm_input GCA_020859995.1_ASM2085999v1_genomic.fna/checkm_result
[2023-06-29 09:03:41,247] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:41,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:41,271] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:41,272] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:41,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020859995.1_ASM2085999v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:41,273] [INFO] Task started: Blastn
[2023-06-29 09:03:41,273] [INFO] Running command: blastn -query GCA_020859995.1_ASM2085999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17ba8b27-ad10-4eaf-9e70-e00795f5abc9/dqc_reference/reference_markers_gtdb.fasta -out GCA_020859995.1_ASM2085999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:42,387] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:42,397] [INFO] Selected 32 target genomes.
[2023-06-29 09:03:42,397] [INFO] Target genome list was writen to GCA_020859995.1_ASM2085999v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:42,438] [INFO] Task started: fastANI
[2023-06-29 09:03:42,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg966fb3d2-f08a-4a4f-92de-38fdd0b37539/GCA_020859995.1_ASM2085999v1_genomic.fna.gz --refList GCA_020859995.1_ASM2085999v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020859995.1_ASM2085999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:03:58,943] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:58,957] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:03:58,958] [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_001941045.1	s__Choladocola sp001941045	77.1526	97	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363135.1	s__Choladousia sp902363135	77.0657	110	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	-
GCA_003612585.1	s__Choladousia sp003612585	77.0191	89	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491565.1	s__Choladousia sp002491565	76.891	111	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712785.1	s__Choladousia intestinavium	76.6788	68	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.61	98.61	0.86	0.86	2	-
GCA_019115125.1	s__Blautia_A faecipullorum	76.3602	59	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.90	97.90	0.82	0.82	2	-
GCF_002160765.1	s__Merdisoma faecalis	76.304	74	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.59	98.32	0.91	0.81	8	-
GCA_900770325.1	s__Merdiplasma sp900770325	76.1948	54	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711815.1	s__Egerieimonas intestinavium	76.1563	55	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:03:58,960] [INFO] GTDB search result was written to GCA_020859995.1_ASM2085999v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:03:58,960] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:03:58,963] [INFO] DFAST_QC result json was written to GCA_020859995.1_ASM2085999v1_genomic.fna/dqc_result.json
[2023-06-29 09:03:58,963] [INFO] DFAST_QC completed!
[2023-06-29 09:03:58,963] [INFO] Total running time: 0h1m26s