[2023-06-05 18:35:07,403] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:35:07,410] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:35:07,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f3ec96e-9e69-46c9-b27c-76ca6197e001/dqc_reference
[2023-06-05 18:35:09,286] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:35:09,286] [INFO] Task started: Prodigal
[2023-06-05 18:35:09,287] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c23ea8c-2ebe-4baf-8976-fcceb3b7e96f/GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:35:11,739] [INFO] Task succeeded: Prodigal
[2023-06-05 18:35:11,739] [INFO] Task started: HMMsearch
[2023-06-05 18:35:11,739] [INFO] Running command: hmmsearch --tblout GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f3ec96e-9e69-46c9-b27c-76ca6197e001/dqc_reference/reference_markers.hmm GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:35:11,924] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:35:11,925] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4c23ea8c-2ebe-4baf-8976-fcceb3b7e96f/GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-05 18:35:11,942] [INFO] Query marker FASTA was written to GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-05 18:35:11,943] [INFO] Task started: Blastn
[2023-06-05 18:35:11,943] [INFO] Running command: blastn -query GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f3ec96e-9e69-46c9-b27c-76ca6197e001/dqc_reference/reference_markers.fasta -out GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:12,470] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:12,473] [INFO] Selected 15 target genomes.
[2023-06-05 18:35:12,473] [INFO] Target genome list was writen to GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-05 18:35:12,477] [INFO] Task started: fastANI
[2023-06-05 18:35:12,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c23ea8c-2ebe-4baf-8976-fcceb3b7e96f/GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:35:18,739] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:18,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f3ec96e-9e69-46c9-b27c-76ca6197e001/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:35:18,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f3ec96e-9e69-46c9-b27c-76ca6197e001/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:35:18,741] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:35:18,741] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:35:18,741] [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 18:35:18,756] [INFO] DFAST Taxonomy check result was written to GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-05 18:35:18,757] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:35:18,757] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:35:18,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f3ec96e-9e69-46c9-b27c-76ca6197e001/dqc_reference/checkm_data
[2023-06-05 18:35:18,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:35:18,777] [INFO] Task started: CheckM
[2023-06-05 18:35:18,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-05 18:35:33,959] [INFO] Task succeeded: CheckM
[2023-06-05 18:35:33,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:35:33,979] [INFO] ===== Completeness check finished =====
[2023-06-05 18:35:33,980] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:35:33,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-05 18:35:33,980] [INFO] Task started: Blastn
[2023-06-05 18:35:33,980] [INFO] Running command: blastn -query GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f3ec96e-9e69-46c9-b27c-76ca6197e001/dqc_reference/reference_markers_gtdb.fasta -out GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:34,433] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:34,437] [INFO] Selected 15 target genomes.
[2023-06-05 18:35:34,437] [INFO] Target genome list was writen to GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:35:34,447] [INFO] Task started: fastANI
[2023-06-05 18:35:34,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c23ea8c-2ebe-4baf-8976-fcceb3b7e96f/GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:35:38,027] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:38,039] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:35:38,039] [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_013333035.2	s__CAG-793 sp013333035	96.6278	324	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	97.61	97.49	0.90	0.89	4	conclusive
GCA_013333395.2	s__CAG-793 sp013333395	89.7105	187	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	96.98	96.69	0.67	0.58	4	-
GCA_000433915.1	s__CAG-793 sp000433915	77.5922	93	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	98.87	98.80	0.92	0.89	3	-
GCA_001915995.1	s__CAG-269 sp001915995	77.0903	76	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525075.1	s__CAG-269 sp003525075	77.05	70	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.02	98.89	0.90	0.88	5	-
GCA_000437215.1	s__CAG-269 sp000437215	76.72	65	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.98	98.94	0.85	0.85	3	-
GCA_003534295.1	s__CAG-273 sp003534295	76.45	59	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.76	98.52	0.84	0.83	5	-
GCA_017510825.1	s__CAG-793 sp017510825	76.3171	73	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900758165.1	s__CAG-245 sp900758165	76.2548	54	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245	95.0	98.95	98.95	0.76	0.76	2	-
GCA_904420285.1	s__CAG-273 sp904420285	76.0596	53	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002372935.1	s__CAG-269 sp002372935	75.8797	57	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:35:38,041] [INFO] GTDB search result was written to GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-05 18:35:38,042] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:35:38,055] [INFO] DFAST_QC result json was written to GCA_916720175.1_SRR15235658_bin.14_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-05 18:35:38,055] [INFO] DFAST_QC completed!
[2023-06-05 18:35:38,055] [INFO] Total running time: 0h0m31s