[2023-06-16 19:08:24,026] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:08:24,029] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:08:24,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9d584d0-d572-4d20-a462-e02b7db41e64/dqc_reference
[2023-06-16 19:08:25,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:08:25,284] [INFO] Task started: Prodigal
[2023-06-16 19:08:25,284] [INFO] Running command: gunzip -c /var/lib/cwl/stg5084df1e-d53e-45a9-8b3d-919b47f97d07/GCA_003640285.1_ASM364028v1_genomic.fna.gz | prodigal -d GCA_003640285.1_ASM364028v1_genomic.fna/cds.fna -a GCA_003640285.1_ASM364028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:08:42,609] [INFO] Task succeeded: Prodigal
[2023-06-16 19:08:42,609] [INFO] Task started: HMMsearch
[2023-06-16 19:08:42,609] [INFO] Running command: hmmsearch --tblout GCA_003640285.1_ASM364028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9d584d0-d572-4d20-a462-e02b7db41e64/dqc_reference/reference_markers.hmm GCA_003640285.1_ASM364028v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:08:43,098] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:08:43,099] [INFO] Found 6/6 markers.
[2023-06-16 19:08:43,181] [INFO] Query marker FASTA was written to GCA_003640285.1_ASM364028v1_genomic.fna/markers.fasta
[2023-06-16 19:08:43,181] [INFO] Task started: Blastn
[2023-06-16 19:08:43,181] [INFO] Running command: blastn -query GCA_003640285.1_ASM364028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9d584d0-d572-4d20-a462-e02b7db41e64/dqc_reference/reference_markers.fasta -out GCA_003640285.1_ASM364028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:08:43,843] [INFO] Task succeeded: Blastn
[2023-06-16 19:08:43,847] [INFO] Selected 57 target genomes.
[2023-06-16 19:08:43,848] [INFO] Target genome list was writen to GCA_003640285.1_ASM364028v1_genomic.fna/target_genomes.txt
[2023-06-16 19:08:43,943] [INFO] Task started: fastANI
[2023-06-16 19:08:43,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg5084df1e-d53e-45a9-8b3d-919b47f97d07/GCA_003640285.1_ASM364028v1_genomic.fna.gz --refList GCA_003640285.1_ASM364028v1_genomic.fna/target_genomes.txt --output GCA_003640285.1_ASM364028v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:09:16,310] [INFO] Task succeeded: fastANI
[2023-06-16 19:09:16,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9d584d0-d572-4d20-a462-e02b7db41e64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:09:16,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9d584d0-d572-4d20-a462-e02b7db41e64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:09:16,321] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:09:16,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:09:16,321] [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
Lachnoanaerobaculum saburreum	strain=DSM 3986	GCA_000185385.1	467210	467210	type	True	94.5044	760	2356	95	below_threshold
Lachnoanaerobaculum gingivalis	strain=KCOM 2030	GCA_003862475.1	2490855	2490855	type	True	87.9635	712	2356	95	below_threshold
Lachnoanaerobaculum orale	strain=DSM 24553	GCA_003862485.1	979627	979627	type	True	85.9771	675	2356	95	below_threshold
Lachnoanaerobaculum umeaense	strain=DSM 23576 = CCUG 58757	GCA_003589745.1	617123	617123	type	True	83.8393	656	2356	95	below_threshold
Lachnoanaerobaculum umeaense	strain=DSM 23576	GCA_003254255.1	617123	617123	type	True	83.8024	623	2356	95	below_threshold
Catonella morbi	strain=ATCC 51271	GCA_000160035.2	43997	43997	type	True	81.5548	153	2356	95	below_threshold
Johnsonella ignava	strain=ATCC 51276	GCA_000235445.1	43995	43995	type	True	79.0654	168	2356	95	below_threshold
Peptoanaerobacter stomatis	strain=ACC19a	GCA_000238115.1	796937	796937	type	True	79.0208	83	2356	95	below_threshold
Catonella massiliensis	strain=Marseille-Q4567	GCA_016651435.1	2799636	2799636	type	True	78.6724	93	2356	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	74.7816	52	2356	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	74.7384	50	2356	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:09:16,323] [INFO] DFAST Taxonomy check result was written to GCA_003640285.1_ASM364028v1_genomic.fna/tc_result.tsv
[2023-06-16 19:09:16,324] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:09:16,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:09:16,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9d584d0-d572-4d20-a462-e02b7db41e64/dqc_reference/checkm_data
[2023-06-16 19:09:16,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:09:16,421] [INFO] Task started: CheckM
[2023-06-16 19:09:16,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003640285.1_ASM364028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003640285.1_ASM364028v1_genomic.fna/checkm_input GCA_003640285.1_ASM364028v1_genomic.fna/checkm_result
[2023-06-16 19:10:13,206] [INFO] Task succeeded: CheckM
[2023-06-16 19:10:13,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 245.36%
Strain heterogeneity: 25.11%
--------------------------------------------------------------------------------
[2023-06-16 19:10:13,244] [INFO] ===== Completeness check finished =====
[2023-06-16 19:10:13,245] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:10:13,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003640285.1_ASM364028v1_genomic.fna/markers.fasta)
[2023-06-16 19:10:13,246] [INFO] Task started: Blastn
[2023-06-16 19:10:13,246] [INFO] Running command: blastn -query GCA_003640285.1_ASM364028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9d584d0-d572-4d20-a462-e02b7db41e64/dqc_reference/reference_markers_gtdb.fasta -out GCA_003640285.1_ASM364028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:10:14,295] [INFO] Task succeeded: Blastn
[2023-06-16 19:10:14,300] [INFO] Selected 41 target genomes.
[2023-06-16 19:10:14,300] [INFO] Target genome list was writen to GCA_003640285.1_ASM364028v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:10:14,378] [INFO] Task started: fastANI
[2023-06-16 19:10:14,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg5084df1e-d53e-45a9-8b3d-919b47f97d07/GCA_003640285.1_ASM364028v1_genomic.fna.gz --refList GCA_003640285.1_ASM364028v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003640285.1_ASM364028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:10:36,899] [INFO] Task succeeded: fastANI
[2023-06-16 19:10:36,912] [INFO] Found 16 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-16 19:10:36,912] [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_900766185.1	s__Johnsonella sp900766185	95.8574	491	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Johnsonella	95.0	97.99	97.99	0.89	0.89	2	inconclusive
GCA_000209465.1	s__Lachnoanaerobaculum sp000209465	95.2343	796	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	98.01	98.01	0.91	0.91	2	inconclusive
GCF_000185385.1	s__Lachnoanaerobaculum saburreum	94.581	757	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	97.52	97.46	0.88	0.85	3	-
GCA_900167215.1	s__Peptoanaerobacter yurii	93.4739	185	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Peptoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373785.1	s__Johnsonella sp905373785	92.9421	387	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Johnsonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296385.1	s__Lachnoanaerobaculum sp000296385	88.844	709	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	96.95	96.95	0.89	0.89	2	-
GCF_003862475.1	s__Lachnoanaerobaculum gingivalis	87.9402	713	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000287675.1	s__Lachnoanaerobaculum sp000287675	87.671	674	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	96.71	96.71	0.86	0.86	2	-
GCA_000146855.1	s__Peptoanaerobacter margaretiae	86.8893	178	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Peptoanaerobacter	95.0	97.24	97.24	0.94	0.94	2	-
GCF_003862485.1	s__Lachnoanaerobaculum orale	85.96	676	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	95.98	95.69	0.85	0.82	6	-
GCF_003589745.1	s__Lachnoanaerobaculum umeaense	83.8333	655	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000160035.2	s__Catonella morbi	81.5237	154	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235445.1	s__Johnsonella ignava	79.0654	168	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Johnsonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238115.1	s__Peptoanaerobacter stomatis	78.9659	84	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Peptoanaerobacter	95.0	95.77	95.04	0.85	0.83	5	-
GCF_016651435.1	s__Catonella massiliensis	78.6521	94	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella	95.0	95.56	95.38	0.94	0.93	3	-
GCF_000439105.1	s__Terrisporobacter glycolicus	74.7816	52	2356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-16 19:10:36,914] [INFO] GTDB search result was written to GCA_003640285.1_ASM364028v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:10:36,915] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:10:36,919] [INFO] DFAST_QC result json was written to GCA_003640285.1_ASM364028v1_genomic.fna/dqc_result.json
[2023-06-16 19:10:36,919] [INFO] DFAST_QC completed!
[2023-06-16 19:10:36,919] [INFO] Total running time: 0h2m13s