[2024-01-25 19:12:35,753] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:35,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:35,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg630c0c63-bdc3-49bb-86bb-2340a121efea/dqc_reference
[2024-01-25 19:12:36,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:36,908] [INFO] Task started: Prodigal
[2024-01-25 19:12:36,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgd033bd06-a884-4302-8d9a-be38248ff686/GCF_014337175.1_ASM1433717v1_genomic.fna.gz | prodigal -d GCF_014337175.1_ASM1433717v1_genomic.fna/cds.fna -a GCF_014337175.1_ASM1433717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:45,074] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:45,075] [INFO] Task started: HMMsearch
[2024-01-25 19:12:45,075] [INFO] Running command: hmmsearch --tblout GCF_014337175.1_ASM1433717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg630c0c63-bdc3-49bb-86bb-2340a121efea/dqc_reference/reference_markers.hmm GCF_014337175.1_ASM1433717v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:45,310] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:45,311] [INFO] Found 6/6 markers.
[2024-01-25 19:12:45,340] [INFO] Query marker FASTA was written to GCF_014337175.1_ASM1433717v1_genomic.fna/markers.fasta
[2024-01-25 19:12:45,340] [INFO] Task started: Blastn
[2024-01-25 19:12:45,340] [INFO] Running command: blastn -query GCF_014337175.1_ASM1433717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg630c0c63-bdc3-49bb-86bb-2340a121efea/dqc_reference/reference_markers.fasta -out GCF_014337175.1_ASM1433717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:45,943] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:45,946] [INFO] Selected 30 target genomes.
[2024-01-25 19:12:45,946] [INFO] Target genome list was writen to GCF_014337175.1_ASM1433717v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:45,963] [INFO] Task started: fastANI
[2024-01-25 19:12:45,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgd033bd06-a884-4302-8d9a-be38248ff686/GCF_014337175.1_ASM1433717v1_genomic.fna.gz --refList GCF_014337175.1_ASM1433717v1_genomic.fna/target_genomes.txt --output GCF_014337175.1_ASM1433717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:04,287] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:04,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg630c0c63-bdc3-49bb-86bb-2340a121efea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:04,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg630c0c63-bdc3-49bb-86bb-2340a121efea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:04,298] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:13:04,298] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:13:04,298] [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
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	81.9845	92	1190	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	81.3457	89	1190	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	81.25	98	1190	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	80.697	64	1190	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	80.6926	65	1190	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	80.5801	76	1190	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	80.3813	130	1190	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	80.0234	61	1190	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	79.0088	83	1190	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	78.9678	56	1190	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	78.7628	116	1190	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	78.6875	52	1190	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	78.0677	52	1190	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	77.7091	163	1190	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.6176	92	1190	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	76.3382	59	1190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:13:04,301] [INFO] DFAST Taxonomy check result was written to GCF_014337175.1_ASM1433717v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:04,301] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:04,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:04,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg630c0c63-bdc3-49bb-86bb-2340a121efea/dqc_reference/checkm_data
[2024-01-25 19:13:04,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:04,345] [INFO] Task started: CheckM
[2024-01-25 19:13:04,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014337175.1_ASM1433717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014337175.1_ASM1433717v1_genomic.fna/checkm_input GCF_014337175.1_ASM1433717v1_genomic.fna/checkm_result
[2024-01-25 19:13:33,169] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:33,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:33,256] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:33,256] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:33,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014337175.1_ASM1433717v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:33,257] [INFO] Task started: Blastn
[2024-01-25 19:13:33,257] [INFO] Running command: blastn -query GCF_014337175.1_ASM1433717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg630c0c63-bdc3-49bb-86bb-2340a121efea/dqc_reference/reference_markers_gtdb.fasta -out GCF_014337175.1_ASM1433717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:34,425] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:34,428] [INFO] Selected 9 target genomes.
[2024-01-25 19:13:34,428] [INFO] Target genome list was writen to GCF_014337175.1_ASM1433717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:34,468] [INFO] Task started: fastANI
[2024-01-25 19:13:34,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgd033bd06-a884-4302-8d9a-be38248ff686/GCF_014337175.1_ASM1433717v1_genomic.fna.gz --refList GCF_014337175.1_ASM1433717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014337175.1_ASM1433717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:40,820] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:40,826] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:40,827] [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	96.5573	806	1190	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	92.7822	599	1190	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	89.8595	873	1190	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	88.0419	710	1190	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	87.3866	675	1190	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	86.6943	646	1190	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	85.7279	435	1190	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_900551115.1	s__CAG-510 sp900551115	77.634	125	1190	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473445.1	s__Acetatifactor sp017473445	77.3318	106	1190	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:40,828] [INFO] GTDB search result was written to GCF_014337175.1_ASM1433717v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:40,828] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:40,831] [INFO] DFAST_QC result json was written to GCF_014337175.1_ASM1433717v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:40,831] [INFO] DFAST_QC completed!
[2024-01-25 19:13:40,831] [INFO] Total running time: 0h1m5s