[2023-06-18 18:10:31,297] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:31,299] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:31,300] [INFO] DQC Reference Directory: /var/lib/cwl/stge5161eff-a3ff-4dbc-86f5-980a95f59f3c/dqc_reference
[2023-06-18 18:10:32,643] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:32,644] [INFO] Task started: Prodigal
[2023-06-18 18:10:32,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg998b0264-caff-4e9d-8958-325448652765/GCA_029059705.1_ASM2905970v1_genomic.fna.gz | prodigal -d GCA_029059705.1_ASM2905970v1_genomic.fna/cds.fna -a GCA_029059705.1_ASM2905970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:36,132] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:36,133] [INFO] Task started: HMMsearch
[2023-06-18 18:10:36,133] [INFO] Running command: hmmsearch --tblout GCA_029059705.1_ASM2905970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5161eff-a3ff-4dbc-86f5-980a95f59f3c/dqc_reference/reference_markers.hmm GCA_029059705.1_ASM2905970v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:36,396] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:36,397] [INFO] Found 6/6 markers.
[2023-06-18 18:10:36,420] [INFO] Query marker FASTA was written to GCA_029059705.1_ASM2905970v1_genomic.fna/markers.fasta
[2023-06-18 18:10:36,420] [INFO] Task started: Blastn
[2023-06-18 18:10:36,420] [INFO] Running command: blastn -query GCA_029059705.1_ASM2905970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5161eff-a3ff-4dbc-86f5-980a95f59f3c/dqc_reference/reference_markers.fasta -out GCA_029059705.1_ASM2905970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:37,003] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:37,009] [INFO] Selected 25 target genomes.
[2023-06-18 18:10:37,010] [INFO] Target genome list was writen to GCA_029059705.1_ASM2905970v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:37,014] [INFO] Task started: fastANI
[2023-06-18 18:10:37,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg998b0264-caff-4e9d-8958-325448652765/GCA_029059705.1_ASM2905970v1_genomic.fna.gz --refList GCA_029059705.1_ASM2905970v1_genomic.fna/target_genomes.txt --output GCA_029059705.1_ASM2905970v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:54,018] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:54,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5161eff-a3ff-4dbc-86f5-980a95f59f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:54,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5161eff-a3ff-4dbc-86f5-980a95f59f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:54,021] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:54,021] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:10:54,021] [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
--------------------------------------------------------------------------------
[2023-06-18 18:10:54,023] [INFO] DFAST Taxonomy check result was written to GCA_029059705.1_ASM2905970v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:54,024] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:54,024] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:54,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5161eff-a3ff-4dbc-86f5-980a95f59f3c/dqc_reference/checkm_data
[2023-06-18 18:10:54,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:54,061] [INFO] Task started: CheckM
[2023-06-18 18:10:54,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_029059705.1_ASM2905970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_029059705.1_ASM2905970v1_genomic.fna/checkm_input GCA_029059705.1_ASM2905970v1_genomic.fna/checkm_result
[2023-06-18 18:11:12,652] [INFO] Task succeeded: CheckM
[2023-06-18 18:11:12,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:11:12,680] [INFO] ===== Completeness check finished =====
[2023-06-18 18:11:12,681] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:11:12,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_029059705.1_ASM2905970v1_genomic.fna/markers.fasta)
[2023-06-18 18:11:12,682] [INFO] Task started: Blastn
[2023-06-18 18:11:12,682] [INFO] Running command: blastn -query GCA_029059705.1_ASM2905970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5161eff-a3ff-4dbc-86f5-980a95f59f3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_029059705.1_ASM2905970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:11:13,484] [INFO] Task succeeded: Blastn
[2023-06-18 18:11:13,490] [INFO] Selected 14 target genomes.
[2023-06-18 18:11:13,490] [INFO] Target genome list was writen to GCA_029059705.1_ASM2905970v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:11:13,497] [INFO] Task started: fastANI
[2023-06-18 18:11:13,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg998b0264-caff-4e9d-8958-325448652765/GCA_029059705.1_ASM2905970v1_genomic.fna.gz --refList GCA_029059705.1_ASM2905970v1_genomic.fna/target_genomes_gtdb.txt --output GCA_029059705.1_ASM2905970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:11:17,588] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:17,607] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 18:11:17,607] [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_910586065.1	s__Coproplasma sp910586065	83.0257	374	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587005.1	s__Coproplasma sp910587005	79.3587	228	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014805025.1	s__Coproplasma sp014805025	78.8038	161	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587015.1	s__Coproplasma sp910587015	78.7736	227	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013316055.1	s__Coproplasma sp013316055	78.6532	164	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	97.79	97.79	0.95	0.95	2	-
GCA_910577375.1	s__Coproplasma sp910577375	78.4331	174	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585785.1	s__Coproplasma sp910585785	78.4115	179	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579585.1	s__Coproplasma sp910579585	78.3869	162	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578145.1	s__Coproplasma sp910578145	78.2	174	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588685.1	s__Coproplasma sp910588685	77.9617	136	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587825.1	s__Coproplasma sp910587825	77.7263	128	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003979335.1	s__Coproplasma sp003979335	77.4883	65	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	97.84	97.84	0.86	0.86	2	-
GCA_018712135.1	s__Coproplasma avicola	77.0705	80	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:11:17,609] [INFO] GTDB search result was written to GCA_029059705.1_ASM2905970v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:11:17,610] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:11:17,613] [INFO] DFAST_QC result json was written to GCA_029059705.1_ASM2905970v1_genomic.fna/dqc_result.json
[2023-06-18 18:11:17,613] [INFO] DFAST_QC completed!
[2023-06-18 18:11:17,613] [INFO] Total running time: 0h0m46s