[2023-06-29 00:23:17,955] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:23:17,957] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:23:17,957] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc84e20b-b827-46e1-bccc-4b3218d48752/dqc_reference
[2023-06-29 00:23:19,259] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:23:19,260] [INFO] Task started: Prodigal
[2023-06-29 00:23:19,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ac61d94-57c5-44a5-afad-11a7ef009592/GCA_020025615.1_ASM2002561v1_genomic.fna.gz | prodigal -d GCA_020025615.1_ASM2002561v1_genomic.fna/cds.fna -a GCA_020025615.1_ASM2002561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:23:23,484] [INFO] Task succeeded: Prodigal
[2023-06-29 00:23:23,484] [INFO] Task started: HMMsearch
[2023-06-29 00:23:23,484] [INFO] Running command: hmmsearch --tblout GCA_020025615.1_ASM2002561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc84e20b-b827-46e1-bccc-4b3218d48752/dqc_reference/reference_markers.hmm GCA_020025615.1_ASM2002561v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:23:23,705] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:23:23,707] [INFO] Found 6/6 markers.
[2023-06-29 00:23:23,730] [INFO] Query marker FASTA was written to GCA_020025615.1_ASM2002561v1_genomic.fna/markers.fasta
[2023-06-29 00:23:23,731] [INFO] Task started: Blastn
[2023-06-29 00:23:23,731] [INFO] Running command: blastn -query GCA_020025615.1_ASM2002561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc84e20b-b827-46e1-bccc-4b3218d48752/dqc_reference/reference_markers.fasta -out GCA_020025615.1_ASM2002561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:23:24,386] [INFO] Task succeeded: Blastn
[2023-06-29 00:23:24,390] [INFO] Selected 22 target genomes.
[2023-06-29 00:23:24,390] [INFO] Target genome list was writen to GCA_020025615.1_ASM2002561v1_genomic.fna/target_genomes.txt
[2023-06-29 00:23:24,393] [INFO] Task started: fastANI
[2023-06-29 00:23:24,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac61d94-57c5-44a5-afad-11a7ef009592/GCA_020025615.1_ASM2002561v1_genomic.fna.gz --refList GCA_020025615.1_ASM2002561v1_genomic.fna/target_genomes.txt --output GCA_020025615.1_ASM2002561v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:23:34,928] [INFO] Task succeeded: fastANI
[2023-06-29 00:23:34,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc84e20b-b827-46e1-bccc-4b3218d48752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:23:34,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc84e20b-b827-46e1-bccc-4b3218d48752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:23:34,937] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:23:34,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:23:34,937] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.8332	57	459	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.6079	55	459	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:23:34,939] [INFO] DFAST Taxonomy check result was written to GCA_020025615.1_ASM2002561v1_genomic.fna/tc_result.tsv
[2023-06-29 00:23:34,940] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:23:34,940] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:23:34,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc84e20b-b827-46e1-bccc-4b3218d48752/dqc_reference/checkm_data
[2023-06-29 00:23:34,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:23:34,966] [INFO] Task started: CheckM
[2023-06-29 00:23:34,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025615.1_ASM2002561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025615.1_ASM2002561v1_genomic.fna/checkm_input GCA_020025615.1_ASM2002561v1_genomic.fna/checkm_result
[2023-06-29 00:23:54,745] [INFO] Task succeeded: CheckM
[2023-06-29 00:23:54,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:23:54,773] [INFO] ===== Completeness check finished =====
[2023-06-29 00:23:54,773] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:23:54,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025615.1_ASM2002561v1_genomic.fna/markers.fasta)
[2023-06-29 00:23:54,774] [INFO] Task started: Blastn
[2023-06-29 00:23:54,774] [INFO] Running command: blastn -query GCA_020025615.1_ASM2002561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc84e20b-b827-46e1-bccc-4b3218d48752/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025615.1_ASM2002561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:23:55,910] [INFO] Task succeeded: Blastn
[2023-06-29 00:23:55,915] [INFO] Selected 24 target genomes.
[2023-06-29 00:23:55,915] [INFO] Target genome list was writen to GCA_020025615.1_ASM2002561v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:23:55,921] [INFO] Task started: fastANI
[2023-06-29 00:23:55,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac61d94-57c5-44a5-afad-11a7ef009592/GCA_020025615.1_ASM2002561v1_genomic.fna.gz --refList GCA_020025615.1_ASM2002561v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025615.1_ASM2002561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:24:05,008] [INFO] Task succeeded: fastANI
[2023-06-29 00:24:05,051] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:24:05,051] [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_017473225.1	s__Faecousia sp017473225	79.9682	109	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622995.1	s__Faecousia sp017622995	79.5927	154	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712645.1	s__Faecousia faecavium	79.5455	160	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017457285.1	s__Faecousia sp017457285	79.5195	88	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461445.1	s__Faecousia sp017461445	79.464	177	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562395.1	s__Faecousia sp004562395	79.3922	132	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544945.1	s__Faecousia sp900544945	79.385	140	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
GCA_900540635.1	s__Faecousia sp900540635	79.2713	161	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.77	97.74	0.82	0.81	3	-
GCA_900762245.1	s__Faecousia sp900762245	79.2632	138	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465745.1	s__Faecousia sp017465745	79.1245	147	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555705.1	s__Faecousia sp004555705	79.0848	153	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547405.1	s__Faecousia sp900547405	79.0586	144	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.15	96.95	0.86	0.86	5	-
GCA_000434635.1	s__Faecousia sp000434635	79.0582	155	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.30	97.16	0.81	0.81	4	-
GCA_002436765.1	s__Faecousia sp002436765	78.9579	140	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_015067615.1	s__Faecousia sp015067615	78.937	158	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409205.1	s__Faecousia sp017409205	78.9181	128	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553805.1	s__Faecousia sp900553805	78.9086	112	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.76	97.76	0.51	0.51	2	-
GCA_017516785.1	s__Faecousia sp017516785	78.8337	114	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017939025.1	s__Faecousia sp017939025	78.8015	99	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437585.1	s__Faecousia sp002437585	78.764	143	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.35	99.16	0.96	0.95	3	-
GCA_017436785.1	s__Faecousia sp017436785	78.699	140	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549705.1	s__Faecousia sp900549705	78.6658	116	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.98	96.52	0.84	0.77	3	-
GCA_900770015.1	s__Faecousia sp900770015	78.5768	116	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302405.1	s__Faecousia sp016302405	78.4908	126	459	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:24:05,055] [INFO] GTDB search result was written to GCA_020025615.1_ASM2002561v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:24:05,055] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:24:05,061] [INFO] DFAST_QC result json was written to GCA_020025615.1_ASM2002561v1_genomic.fna/dqc_result.json
[2023-06-29 00:24:05,062] [INFO] DFAST_QC completed!
[2023-06-29 00:24:05,062] [INFO] Total running time: 0h0m47s