[2024-01-24 13:40:43,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,412] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d6ac168-6ab9-4eca-87b2-196cd9736647/dqc_reference
[2024-01-24 13:40:44,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,827] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg8875a30a-0925-4ae7-8299-d4a151d55f83/GCF_003432035.1_ASM343203v1_genomic.fna.gz | prodigal -d GCF_003432035.1_ASM343203v1_genomic.fna/cds.fna -a GCF_003432035.1_ASM343203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,949] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,949] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,949] [INFO] Running command: hmmsearch --tblout GCF_003432035.1_ASM343203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d6ac168-6ab9-4eca-87b2-196cd9736647/dqc_reference/reference_markers.hmm GCF_003432035.1_ASM343203v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:59,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:59,349] [INFO] Found 6/6 markers.
[2024-01-24 13:40:59,403] [INFO] Query marker FASTA was written to GCF_003432035.1_ASM343203v1_genomic.fna/markers.fasta
[2024-01-24 13:40:59,403] [INFO] Task started: Blastn
[2024-01-24 13:40:59,403] [INFO] Running command: blastn -query GCF_003432035.1_ASM343203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d6ac168-6ab9-4eca-87b2-196cd9736647/dqc_reference/reference_markers.fasta -out GCF_003432035.1_ASM343203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:00,102] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:00,105] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:00,105] [INFO] Target genome list was writen to GCF_003432035.1_ASM343203v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:00,110] [INFO] Task started: fastANI
[2024-01-24 13:41:00,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg8875a30a-0925-4ae7-8299-d4a151d55f83/GCF_003432035.1_ASM343203v1_genomic.fna.gz --refList GCF_003432035.1_ASM343203v1_genomic.fna/target_genomes.txt --output GCF_003432035.1_ASM343203v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:12,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:12,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d6ac168-6ab9-4eca-87b2-196cd9736647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:12,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d6ac168-6ab9-4eca-87b2-196cd9736647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:12,035] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:12,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:12,035] [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
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	79.5736	546	1898	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	79.4676	542	1898	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	79.429	543	1898	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	79.3597	554	1898	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	78.8906	492	1898	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	78.3642	260	1898	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	78.3232	259	1898	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	78.2824	231	1898	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	77.4573	109	1898	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.973	64	1898	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.8775	66	1898	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	76.819	62	1898	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	76.6012	54	1898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:12,037] [INFO] DFAST Taxonomy check result was written to GCF_003432035.1_ASM343203v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:12,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:12,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:12,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d6ac168-6ab9-4eca-87b2-196cd9736647/dqc_reference/checkm_data
[2024-01-24 13:41:12,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:12,098] [INFO] Task started: CheckM
[2024-01-24 13:41:12,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003432035.1_ASM343203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003432035.1_ASM343203v1_genomic.fna/checkm_input GCF_003432035.1_ASM343203v1_genomic.fna/checkm_result
[2024-01-24 13:41:57,712] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:57,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:57,736] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:57,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:57,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003432035.1_ASM343203v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:57,738] [INFO] Task started: Blastn
[2024-01-24 13:41:57,738] [INFO] Running command: blastn -query GCF_003432035.1_ASM343203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d6ac168-6ab9-4eca-87b2-196cd9736647/dqc_reference/reference_markers_gtdb.fasta -out GCF_003432035.1_ASM343203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:58,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:58,848] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:58,848] [INFO] Target genome list was writen to GCF_003432035.1_ASM343203v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:58,872] [INFO] Task started: fastANI
[2024-01-24 13:41:58,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg8875a30a-0925-4ae7-8299-d4a151d55f83/GCF_003432035.1_ASM343203v1_genomic.fna.gz --refList GCF_003432035.1_ASM343203v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003432035.1_ASM343203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:09,580] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:09,592] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:09,592] [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_003432035.1	s__Lacrimispora indica	100.0	1886	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013036995.1	s__Lacrimispora xylanolytica_A	87.9628	1282	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057705.1	s__Lacrimispora sp015057705	87.288	1133	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057715.1	s__Lacrimispora sp015057715	87.1118	1142	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934545.1	s__Lacrimispora xylanolytica	87.1055	1281	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	98.92	98.92	0.97	0.97	2	-
GCA_009712635.1	s__Lacrimispora sp009712635	87.0712	1251	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057775.1	s__Lacrimispora sp015057775	86.959	978	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900205965.1	s__Lacrimispora amygdalina_A	86.4229	1227	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797975.1	s__Lacrimispora celerecrescens	79.3449	552	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.58	99.58	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:09,594] [INFO] GTDB search result was written to GCF_003432035.1_ASM343203v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:09,594] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:09,599] [INFO] DFAST_QC result json was written to GCF_003432035.1_ASM343203v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:09,599] [INFO] DFAST_QC completed!
[2024-01-24 13:42:09,599] [INFO] Total running time: 0h1m26s