[2023-06-28 08:22:08,222] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:22:08,227] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:22:08,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg109d1a9c-c68e-48d2-9a9f-a14645331127/dqc_reference
[2023-06-28 08:22:10,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:22:10,501] [INFO] Task started: Prodigal
[2023-06-28 08:22:10,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg21f83925-8640-473c-a24c-ad5ecae271f3/GCA_944384815.1_E14_bin44_genomic.fna.gz | prodigal -d GCA_944384815.1_E14_bin44_genomic.fna/cds.fna -a GCA_944384815.1_E14_bin44_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:22:15,872] [INFO] Task succeeded: Prodigal
[2023-06-28 08:22:15,873] [INFO] Task started: HMMsearch
[2023-06-28 08:22:15,873] [INFO] Running command: hmmsearch --tblout GCA_944384815.1_E14_bin44_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg109d1a9c-c68e-48d2-9a9f-a14645331127/dqc_reference/reference_markers.hmm GCA_944384815.1_E14_bin44_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:22:16,123] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:22:16,125] [INFO] Found 6/6 markers.
[2023-06-28 08:22:16,150] [INFO] Query marker FASTA was written to GCA_944384815.1_E14_bin44_genomic.fna/markers.fasta
[2023-06-28 08:22:16,150] [INFO] Task started: Blastn
[2023-06-28 08:22:16,151] [INFO] Running command: blastn -query GCA_944384815.1_E14_bin44_genomic.fna/markers.fasta -db /var/lib/cwl/stg109d1a9c-c68e-48d2-9a9f-a14645331127/dqc_reference/reference_markers.fasta -out GCA_944384815.1_E14_bin44_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:22:16,790] [INFO] Task succeeded: Blastn
[2023-06-28 08:22:16,795] [INFO] Selected 18 target genomes.
[2023-06-28 08:22:16,795] [INFO] Target genome list was writen to GCA_944384815.1_E14_bin44_genomic.fna/target_genomes.txt
[2023-06-28 08:22:16,800] [INFO] Task started: fastANI
[2023-06-28 08:22:16,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg21f83925-8640-473c-a24c-ad5ecae271f3/GCA_944384815.1_E14_bin44_genomic.fna.gz --refList GCA_944384815.1_E14_bin44_genomic.fna/target_genomes.txt --output GCA_944384815.1_E14_bin44_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:22:27,399] [INFO] Task succeeded: fastANI
[2023-06-28 08:22:27,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg109d1a9c-c68e-48d2-9a9f-a14645331127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:22:27,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg109d1a9c-c68e-48d2-9a9f-a14645331127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:22:27,408] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:22:27,408] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 08:22:27,408] [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
Hydrogeniiclostridium mannosilyticum	strain=ASD2818	GCA_003268275.1	2764322	2764322	type	True	77.8582	64	651	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	76.8797	53	651	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 08:22:27,410] [INFO] DFAST Taxonomy check result was written to GCA_944384815.1_E14_bin44_genomic.fna/tc_result.tsv
[2023-06-28 08:22:27,410] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:22:27,411] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:22:27,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg109d1a9c-c68e-48d2-9a9f-a14645331127/dqc_reference/checkm_data
[2023-06-28 08:22:27,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:22:27,440] [INFO] Task started: CheckM
[2023-06-28 08:22:27,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944384815.1_E14_bin44_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944384815.1_E14_bin44_genomic.fna/checkm_input GCA_944384815.1_E14_bin44_genomic.fna/checkm_result
[2023-06-28 08:22:49,227] [INFO] Task succeeded: CheckM
[2023-06-28 08:22:49,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:22:49,245] [INFO] ===== Completeness check finished =====
[2023-06-28 08:22:49,246] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:22:49,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944384815.1_E14_bin44_genomic.fna/markers.fasta)
[2023-06-28 08:22:49,246] [INFO] Task started: Blastn
[2023-06-28 08:22:49,247] [INFO] Running command: blastn -query GCA_944384815.1_E14_bin44_genomic.fna/markers.fasta -db /var/lib/cwl/stg109d1a9c-c68e-48d2-9a9f-a14645331127/dqc_reference/reference_markers_gtdb.fasta -out GCA_944384815.1_E14_bin44_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:22:50,295] [INFO] Task succeeded: Blastn
[2023-06-28 08:22:50,299] [INFO] Selected 25 target genomes.
[2023-06-28 08:22:50,300] [INFO] Target genome list was writen to GCA_944384815.1_E14_bin44_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:22:50,338] [INFO] Task started: fastANI
[2023-06-28 08:22:50,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg21f83925-8640-473c-a24c-ad5ecae271f3/GCA_944384815.1_E14_bin44_genomic.fna.gz --refList GCA_944384815.1_E14_bin44_genomic.fna/target_genomes_gtdb.txt --output GCA_944384815.1_E14_bin44_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:23:00,538] [INFO] Task succeeded: fastANI
[2023-06-28 08:23:00,551] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 08:23:00,551] [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_900550095.1	s__UMGS1264 sp900550095	77.5174	101	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1264	95.0	100.00	100.00	0.98	0.98	2	-
GCF_904420555.1	s__Heritagella intestinalis	77.3595	69	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Heritagella	95.0	98.37	96.53	0.95	0.92	4	-
GCA_904399395.1	s__UMGS1264 sp904399395	77.3367	135	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1264	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	77.0934	53	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160025.1	s__Caccousia stercoris	77.0647	71	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	99.23	99.23	0.95	0.95	2	-
GCF_001261775.1	s__Anaeromassilibacillus senegalensis	76.8797	53	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712435.1	s__Caccousia avicola	76.8402	69	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.29	98.29	0.88	0.88	2	-
GCF_002159845.1	s__Anaeromassilibacillus stercoravium	76.7953	60	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	98.79	98.27	0.94	0.87	13	-
GCF_904394685.1	s__Heritagella gallinarum	76.7411	65	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Heritagella	95.0	99.21	99.21	0.89	0.89	2	-
GCA_018715025.1	s__Caccousia avistercoris	76.5162	82	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.39	98.39	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-28 08:23:00,553] [INFO] GTDB search result was written to GCA_944384815.1_E14_bin44_genomic.fna/result_gtdb.tsv
[2023-06-28 08:23:00,553] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:23:00,556] [INFO] DFAST_QC result json was written to GCA_944384815.1_E14_bin44_genomic.fna/dqc_result.json
[2023-06-28 08:23:00,556] [INFO] DFAST_QC completed!
[2023-06-28 08:23:00,556] [INFO] Total running time: 0h0m52s