[2024-01-24 14:14:19,034] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:19,038] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:19,038] [INFO] DQC Reference Directory: /var/lib/cwl/stgec86a0a4-7f1d-480e-9bc2-90f0e1c8143f/dqc_reference
[2024-01-24 14:14:20,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:20,324] [INFO] Task started: Prodigal
[2024-01-24 14:14:20,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg000e9d86-cd17-444a-b6c8-afabeda57d42/GCF_009917485.1_ASM991748v1_genomic.fna.gz | prodigal -d GCF_009917485.1_ASM991748v1_genomic.fna/cds.fna -a GCF_009917485.1_ASM991748v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:32,944] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:32,945] [INFO] Task started: HMMsearch
[2024-01-24 14:14:32,945] [INFO] Running command: hmmsearch --tblout GCF_009917485.1_ASM991748v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec86a0a4-7f1d-480e-9bc2-90f0e1c8143f/dqc_reference/reference_markers.hmm GCF_009917485.1_ASM991748v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,282] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,324] [INFO] Query marker FASTA was written to GCF_009917485.1_ASM991748v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,324] [INFO] Task started: Blastn
[2024-01-24 14:14:33,324] [INFO] Running command: blastn -query GCF_009917485.1_ASM991748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec86a0a4-7f1d-480e-9bc2-90f0e1c8143f/dqc_reference/reference_markers.fasta -out GCF_009917485.1_ASM991748v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:33,985] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:33,989] [INFO] Selected 34 target genomes.
[2024-01-24 14:14:33,989] [INFO] Target genome list was writen to GCF_009917485.1_ASM991748v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:34,005] [INFO] Task started: fastANI
[2024-01-24 14:14:34,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg000e9d86-cd17-444a-b6c8-afabeda57d42/GCF_009917485.1_ASM991748v1_genomic.fna.gz --refList GCF_009917485.1_ASM991748v1_genomic.fna/target_genomes.txt --output GCF_009917485.1_ASM991748v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:53,587] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:53,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec86a0a4-7f1d-480e-9bc2-90f0e1c8143f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:53,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec86a0a4-7f1d-480e-9bc2-90f0e1c8143f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:53,597] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:14:53,598] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:14:53,598] [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
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	78.9708	70	1619	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	78.7647	57	1619	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	78.6962	129	1619	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	78.1594	58	1619	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	77.755	121	1619	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.6419	61	1619	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_002915525.1	341220	341220	suspected-type	True	77.5202	55	1619	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.7167	84	1619	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.623	80	1619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:53,600] [INFO] DFAST Taxonomy check result was written to GCF_009917485.1_ASM991748v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:53,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:53,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:53,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec86a0a4-7f1d-480e-9bc2-90f0e1c8143f/dqc_reference/checkm_data
[2024-01-24 14:14:53,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:53,652] [INFO] Task started: CheckM
[2024-01-24 14:14:53,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009917485.1_ASM991748v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009917485.1_ASM991748v1_genomic.fna/checkm_input GCF_009917485.1_ASM991748v1_genomic.fna/checkm_result
[2024-01-24 14:15:32,155] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:32,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:32,174] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:32,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:32,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009917485.1_ASM991748v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:32,175] [INFO] Task started: Blastn
[2024-01-24 14:15:32,175] [INFO] Running command: blastn -query GCF_009917485.1_ASM991748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec86a0a4-7f1d-480e-9bc2-90f0e1c8143f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009917485.1_ASM991748v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:33,200] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:33,203] [INFO] Selected 11 target genomes.
[2024-01-24 14:15:33,204] [INFO] Target genome list was writen to GCF_009917485.1_ASM991748v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:33,216] [INFO] Task started: fastANI
[2024-01-24 14:15:33,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg000e9d86-cd17-444a-b6c8-afabeda57d42/GCF_009917485.1_ASM991748v1_genomic.fna.gz --refList GCF_009917485.1_ASM991748v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009917485.1_ASM991748v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:42,154] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:42,164] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:42,164] [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_009917485.1	s__CAG-95 sp009917485	100.0	1612	1619	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	conclusive
GCA_003612395.1	s__CAG-95 sp003612395	82.9651	958	1619	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	-
GCA_910587305.1	s__CAG-95 sp910587305	82.694	823	1619	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	-
GCA_910585075.1	s__CAG-95 sp910585075	80.2073	698	1619	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	-
GCA_011959285.1	s__CAG-95 sp011959285	79.8559	365	1619	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.06	99.06	0.84	0.84	2	-
GCA_014804785.1	s__CAG-95 sp014804785	78.4851	351	1619	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	-
GCA_910575075.1	s__14-2 sp910575075	77.9227	95	1619	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.99	99.99	0.99	0.99	4	-
GCA_002492465.1	s__CAG-95 sp002492465	77.8861	271	1619	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	-
GCA_900554925.1	s__CAG-95 sp900554925	77.6398	229	1619	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	-
GCA_017938315.1	s__CAG-95 sp017938315	77.265	137	1619	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	-
GCA_017500935.1	s__Eisenbergiella sp017500935	76.0068	57	1619	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:42,166] [INFO] GTDB search result was written to GCF_009917485.1_ASM991748v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:42,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:42,170] [INFO] DFAST_QC result json was written to GCF_009917485.1_ASM991748v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:42,170] [INFO] DFAST_QC completed!
[2024-01-24 14:15:42,170] [INFO] Total running time: 0h1m23s