[2024-01-24 13:28:01,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,951] [INFO] DQC Reference Directory: /var/lib/cwl/stge3c63c61-071e-409b-89c9-f119461cdb62/dqc_reference
[2024-01-24 13:28:03,369] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,373] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,373] [INFO] Running command: gunzip -c /var/lib/cwl/stgf69609b1-298c-497b-b858-c1d4572e3b6e/GCF_009695995.1_ASM969599v1_genomic.fna.gz | prodigal -d GCF_009695995.1_ASM969599v1_genomic.fna/cds.fna -a GCF_009695995.1_ASM969599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:10,930] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:10,930] [INFO] Task started: HMMsearch
[2024-01-24 13:28:10,930] [INFO] Running command: hmmsearch --tblout GCF_009695995.1_ASM969599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3c63c61-071e-409b-89c9-f119461cdb62/dqc_reference/reference_markers.hmm GCF_009695995.1_ASM969599v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:11,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:11,201] [INFO] Found 6/6 markers.
[2024-01-24 13:28:11,226] [INFO] Query marker FASTA was written to GCF_009695995.1_ASM969599v1_genomic.fna/markers.fasta
[2024-01-24 13:28:11,227] [INFO] Task started: Blastn
[2024-01-24 13:28:11,227] [INFO] Running command: blastn -query GCF_009695995.1_ASM969599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c63c61-071e-409b-89c9-f119461cdb62/dqc_reference/reference_markers.fasta -out GCF_009695995.1_ASM969599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:11,913] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:11,917] [INFO] Selected 31 target genomes.
[2024-01-24 13:28:11,917] [INFO] Target genome list was writen to GCF_009695995.1_ASM969599v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:11,953] [INFO] Task started: fastANI
[2024-01-24 13:28:11,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69609b1-298c-497b-b858-c1d4572e3b6e/GCF_009695995.1_ASM969599v1_genomic.fna.gz --refList GCF_009695995.1_ASM969599v1_genomic.fna/target_genomes.txt --output GCF_009695995.1_ASM969599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:31,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:31,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3c63c61-071e-409b-89c9-f119461cdb62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:31,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3c63c61-071e-409b-89c9-f119461cdb62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:31,117] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:31,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:31,117] [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	78.2268	62	966	95	below_threshold
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	78.2168	70	966	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.6342	100	966	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	77.5598	94	966	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.4782	85	966	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.3823	97	966	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.3287	74	966	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.2259	65	966	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.1343	51	966	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.8996	131	966	95	below_threshold
Blautia producta	strain=JCM 1471	GCA_010669205.1	33035	33035	suspected-type	True	76.8613	50	966	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	76.8554	50	966	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.7332	64	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:31,119] [INFO] DFAST Taxonomy check result was written to GCF_009695995.1_ASM969599v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:31,119] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:31,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:31,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3c63c61-071e-409b-89c9-f119461cdb62/dqc_reference/checkm_data
[2024-01-24 13:28:31,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:31,152] [INFO] Task started: CheckM
[2024-01-24 13:28:31,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695995.1_ASM969599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695995.1_ASM969599v1_genomic.fna/checkm_input GCF_009695995.1_ASM969599v1_genomic.fna/checkm_result
[2024-01-24 13:28:58,721] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:58,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:58,741] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:58,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:58,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695995.1_ASM969599v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:58,743] [INFO] Task started: Blastn
[2024-01-24 13:28:58,743] [INFO] Running command: blastn -query GCF_009695995.1_ASM969599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c63c61-071e-409b-89c9-f119461cdb62/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695995.1_ASM969599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:59,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:59,857] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:59,857] [INFO] Target genome list was writen to GCF_009695995.1_ASM969599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:59,889] [INFO] Task started: fastANI
[2024-01-24 13:28:59,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69609b1-298c-497b-b858-c1d4572e3b6e/GCF_009695995.1_ASM969599v1_genomic.fna.gz --refList GCF_009695995.1_ASM969599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695995.1_ASM969599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:06,528] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:06,537] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:06,537] [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_009695995.1	s__Acetatifactor intestinalis	100.0	964	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.98	96.46	0.81	0.76	18	conclusive
GCA_003447295.1	s__Acetatifactor sp003447295	92.2073	542	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.04	96.84	0.74	0.71	4	-
GCA_003584705.1	s__Acetatifactor sp900066565	88.7942	752	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	-
GCA_900772845.1	s__Acetatifactor sp900772845	87.9251	656	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	95.92	95.92	0.80	0.80	2	-
GCA_002431915.1	s__Acetatifactor sp002431915	87.524	623	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900771995.1	s__Acetatifactor sp900771995	86.5705	618	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766575.1	s__Acetatifactor sp900766575	85.3234	407	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473445.1	s__Acetatifactor sp017473445	77.3192	106	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766365.1	s__CAG-95 sp902766365	76.9575	138	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,539] [INFO] GTDB search result was written to GCF_009695995.1_ASM969599v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:06,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:06,543] [INFO] DFAST_QC result json was written to GCF_009695995.1_ASM969599v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:06,543] [INFO] DFAST_QC completed!
[2024-01-24 13:29:06,543] [INFO] Total running time: 0h1m5s