[2023-06-29 16:18:52,677] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:18:52,680] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:18:52,680] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2d1f085-0ab0-4b6c-8a56-2853410d608e/dqc_reference
[2023-06-29 16:18:54,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:18:54,109] [INFO] Task started: Prodigal
[2023-06-29 16:18:54,110] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb9da7d4-d12f-4714-9890-2ae0e75d4450/GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:18:58,562] [INFO] Task succeeded: Prodigal
[2023-06-29 16:18:58,562] [INFO] Task started: HMMsearch
[2023-06-29 16:18:58,562] [INFO] Running command: hmmsearch --tblout GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2d1f085-0ab0-4b6c-8a56-2853410d608e/dqc_reference/reference_markers.hmm GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:18:58,832] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:18:58,833] [INFO] Found 6/6 markers.
[2023-06-29 16:18:58,861] [INFO] Query marker FASTA was written to GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:18:58,861] [INFO] Task started: Blastn
[2023-06-29 16:18:58,862] [INFO] Running command: blastn -query GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2d1f085-0ab0-4b6c-8a56-2853410d608e/dqc_reference/reference_markers.fasta -out GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:18:59,520] [INFO] Task succeeded: Blastn
[2023-06-29 16:18:59,524] [INFO] Selected 19 target genomes.
[2023-06-29 16:18:59,524] [INFO] Target genome list was writen to GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:18:59,527] [INFO] Task started: fastANI
[2023-06-29 16:18:59,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9da7d4-d12f-4714-9890-2ae0e75d4450/GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:19:11,382] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:11,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2d1f085-0ab0-4b6c-8a56-2853410d608e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:19:11,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2d1f085-0ab0-4b6c-8a56-2853410d608e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:19:11,387] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:19:11,388] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:19:11,388] [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
Phascolarctobacterium succinatutens	strain=YIT 12067	GCA_000188175.1	626940	626940	type	True	79.624	189	491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:19:11,394] [INFO] DFAST Taxonomy check result was written to GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:19:11,395] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:19:11,395] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:19:11,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2d1f085-0ab0-4b6c-8a56-2853410d608e/dqc_reference/checkm_data
[2023-06-29 16:19:11,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:19:11,427] [INFO] Task started: CheckM
[2023-06-29 16:19:11,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:19:32,361] [INFO] Task succeeded: CheckM
[2023-06-29 16:19:32,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:19:32,385] [INFO] ===== Completeness check finished =====
[2023-06-29 16:19:32,385] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:19:32,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:19:32,386] [INFO] Task started: Blastn
[2023-06-29 16:19:32,386] [INFO] Running command: blastn -query GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2d1f085-0ab0-4b6c-8a56-2853410d608e/dqc_reference/reference_markers_gtdb.fasta -out GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:33,228] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:33,233] [INFO] Selected 11 target genomes.
[2023-06-29 16:19:33,233] [INFO] Target genome list was writen to GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:19:33,240] [INFO] Task started: fastANI
[2023-06-29 16:19:33,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9da7d4-d12f-4714-9890-2ae0e75d4450/GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:19:37,096] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:37,106] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:19:37,106] [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_900553055.1	s__Phascolarctobacterium_A sp900553055	100.0	414	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	98.03	96.65	0.77	0.68	4	conclusive
GCA_004558595.1	s__Phascolarctobacterium_A sp004558595	85.2513	343	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562175.1	s__Phascolarctobacterium_A sp004562175	84.1908	200	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905200645.1	s__Phascolarctobacterium_A sp905200645	80.3234	253	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905212365.1	s__Phascolarctobacterium_A sp905212365	80.0354	215	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757795.1	s__Phascolarctobacterium_A sp900757795	79.8644	222	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	97.50	97.50	0.82	0.82	2	-
GCA_000434895.1	s__Phascolarctobacterium_A succinatutens_A	79.7109	191	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	95.38	95.36	0.85	0.80	4	-
GCF_000188175.1	s__Phascolarctobacterium_A succinatutens	79.6671	187	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	97.32	95.06	0.90	0.84	17	-
GCA_900547415.1	s__Phascolarctobacterium_A sp900547415	78.9405	146	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	99.47	98.95	0.94	0.88	3	-
GCA_900552855.1	s__Phascolarctobacterium_A sp900552855	78.494	120	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	99.31	98.81	0.91	0.90	3	-
GCA_900551335.1	s__Phascolarctobacterium_A sp900551335	78.168	137	491	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	96.01	95.96	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-29 16:19:37,108] [INFO] GTDB search result was written to GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:19:37,108] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:19:37,111] [INFO] DFAST_QC result json was written to GCA_937984015.1_ERR209453_bin.4_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:19:37,112] [INFO] DFAST_QC completed!
[2023-06-29 16:19:37,112] [INFO] Total running time: 0h0m44s