[2023-06-05 10:33:35,607] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:33:35,610] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:33:35,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ef38bc7-84e2-4c33-b466-90f883ef5bea/dqc_reference
[2023-06-05 10:33:37,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:33:37,579] [INFO] Task started: Prodigal
[2023-06-05 10:33:37,580] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfefa7d6-171c-4f84-9f0a-2e0f2bdf33b6/GCA_004558935.1_ASM455893v1_genomic.fna.gz | prodigal -d GCA_004558935.1_ASM455893v1_genomic.fna/cds.fna -a GCA_004558935.1_ASM455893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:33:41,708] [INFO] Task succeeded: Prodigal
[2023-06-05 10:33:41,708] [INFO] Task started: HMMsearch
[2023-06-05 10:33:41,708] [INFO] Running command: hmmsearch --tblout GCA_004558935.1_ASM455893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ef38bc7-84e2-4c33-b466-90f883ef5bea/dqc_reference/reference_markers.hmm GCA_004558935.1_ASM455893v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:33:42,030] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:33:42,031] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbfefa7d6-171c-4f84-9f0a-2e0f2bdf33b6/GCA_004558935.1_ASM455893v1_genomic.fna.gz]
[2023-06-05 10:33:42,061] [INFO] Query marker FASTA was written to GCA_004558935.1_ASM455893v1_genomic.fna/markers.fasta
[2023-06-05 10:33:42,061] [INFO] Task started: Blastn
[2023-06-05 10:33:42,061] [INFO] Running command: blastn -query GCA_004558935.1_ASM455893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef38bc7-84e2-4c33-b466-90f883ef5bea/dqc_reference/reference_markers.fasta -out GCA_004558935.1_ASM455893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:33:43,416] [INFO] Task succeeded: Blastn
[2023-06-05 10:33:43,434] [INFO] Selected 23 target genomes.
[2023-06-05 10:33:43,435] [INFO] Target genome list was writen to GCA_004558935.1_ASM455893v1_genomic.fna/target_genomes.txt
[2023-06-05 10:33:43,452] [INFO] Task started: fastANI
[2023-06-05 10:33:43,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfefa7d6-171c-4f84-9f0a-2e0f2bdf33b6/GCA_004558935.1_ASM455893v1_genomic.fna.gz --refList GCA_004558935.1_ASM455893v1_genomic.fna/target_genomes.txt --output GCA_004558935.1_ASM455893v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:33:57,090] [INFO] Task succeeded: fastANI
[2023-06-05 10:33:57,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ef38bc7-84e2-4c33-b466-90f883ef5bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:33:57,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ef38bc7-84e2-4c33-b466-90f883ef5bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:33:57,093] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:33:57,093] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:33:57,093] [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
--------------------------------------------------------------------------------
[2023-06-05 10:33:57,095] [INFO] DFAST Taxonomy check result was written to GCA_004558935.1_ASM455893v1_genomic.fna/tc_result.tsv
[2023-06-05 10:33:57,095] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:33:57,096] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:33:57,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ef38bc7-84e2-4c33-b466-90f883ef5bea/dqc_reference/checkm_data
[2023-06-05 10:33:57,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:33:57,122] [INFO] Task started: CheckM
[2023-06-05 10:33:57,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004558935.1_ASM455893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004558935.1_ASM455893v1_genomic.fna/checkm_input GCA_004558935.1_ASM455893v1_genomic.fna/checkm_result
[2023-06-05 10:34:17,122] [INFO] Task succeeded: CheckM
[2023-06-05 10:34:17,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.03%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:34:17,144] [INFO] ===== Completeness check finished =====
[2023-06-05 10:34:17,144] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:34:17,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004558935.1_ASM455893v1_genomic.fna/markers.fasta)
[2023-06-05 10:34:17,145] [INFO] Task started: Blastn
[2023-06-05 10:34:17,145] [INFO] Running command: blastn -query GCA_004558935.1_ASM455893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef38bc7-84e2-4c33-b466-90f883ef5bea/dqc_reference/reference_markers_gtdb.fasta -out GCA_004558935.1_ASM455893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:18,233] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:18,238] [INFO] Selected 23 target genomes.
[2023-06-05 10:34:18,238] [INFO] Target genome list was writen to GCA_004558935.1_ASM455893v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:34:18,254] [INFO] Task started: fastANI
[2023-06-05 10:34:18,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfefa7d6-171c-4f84-9f0a-2e0f2bdf33b6/GCA_004558935.1_ASM455893v1_genomic.fna.gz --refList GCA_004558935.1_ASM455893v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004558935.1_ASM455893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:34:27,111] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:27,128] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 10:34:27,129] [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_016302005.1	s__Faecousia sp016302005	94.9465	189	390	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_004556205.1	s__Faecousia sp004556205	83.9504	174	390	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_000436735.1	s__CAG-170 sp000436735	80.3731	59	390	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.61	96.80	0.78	0.67	4	-
GCA_905233385.1	s__Faecousia sp905233385	78.8166	108	390	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_905235655.1	s__Faecousia sp905235655	78.707	100	390	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_017405865.1	s__Faecousia sp017405865	78.6724	107	390	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_900544705.1	s__Faecousia sp900544705	78.4545	93	390	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.60	98.49	0.88	0.86	3	-
GCA_900769995.1	s__Faecousia sp900769995	78.4427	88	390	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_017429835.1	s__Faecousia sp017429835	78.4072	113	390	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_900546415.1	s__Faecousia sp900546415	78.0634	101	390	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.49	97.72	0.83	0.81	4	-
GCA_017577345.1	s__Faecousia sp017577345	77.9692	71	390	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_017399355.1	s__Faecousia sp017399355	77.5545	57	390	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:34:27,131] [INFO] GTDB search result was written to GCA_004558935.1_ASM455893v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:34:27,131] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:34:27,134] [INFO] DFAST_QC result json was written to GCA_004558935.1_ASM455893v1_genomic.fna/dqc_result.json
[2023-06-05 10:34:27,135] [INFO] DFAST_QC completed!
[2023-06-05 10:34:27,135] [INFO] Total running time: 0h0m52s