[2023-06-08 13:52:18,269] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:52:18,273] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:52:18,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e0dd9b6-b8de-49ec-9fdc-482faa9b9ff2/dqc_reference
[2023-06-08 13:52:19,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:52:19,495] [INFO] Task started: Prodigal
[2023-06-08 13:52:19,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg06e405b6-4553-499e-83aa-e84e2e674f8a/GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:52:27,872] [INFO] Task succeeded: Prodigal
[2023-06-08 13:52:27,872] [INFO] Task started: HMMsearch
[2023-06-08 13:52:27,873] [INFO] Running command: hmmsearch --tblout GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e0dd9b6-b8de-49ec-9fdc-482faa9b9ff2/dqc_reference/reference_markers.hmm GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:52:28,106] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:52:28,107] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg06e405b6-4553-499e-83aa-e84e2e674f8a/GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 13:52:28,136] [INFO] Query marker FASTA was written to GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:52:28,137] [INFO] Task started: Blastn
[2023-06-08 13:52:28,137] [INFO] Running command: blastn -query GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e0dd9b6-b8de-49ec-9fdc-482faa9b9ff2/dqc_reference/reference_markers.fasta -out GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:28,657] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:28,662] [INFO] Selected 13 target genomes.
[2023-06-08 13:52:28,662] [INFO] Target genome list was writen to GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:52:28,664] [INFO] Task started: fastANI
[2023-06-08 13:52:28,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e405b6-4553-499e-83aa-e84e2e674f8a/GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:52:33,823] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:33,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e0dd9b6-b8de-49ec-9fdc-482faa9b9ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:52:33,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e0dd9b6-b8de-49ec-9fdc-482faa9b9ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:52:33,833] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:52:33,833] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:52:33,833] [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
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.4916	63	331	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.4517	62	331	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	75.825	52	331	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:52:33,836] [INFO] DFAST Taxonomy check result was written to GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:52:33,836] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:52:33,836] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:52:33,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e0dd9b6-b8de-49ec-9fdc-482faa9b9ff2/dqc_reference/checkm_data
[2023-06-08 13:52:33,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:52:33,866] [INFO] Task started: CheckM
[2023-06-08 13:52:33,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:53:02,948] [INFO] Task succeeded: CheckM
[2023-06-08 13:53:02,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:53:02,968] [INFO] ===== Completeness check finished =====
[2023-06-08 13:53:02,968] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:53:02,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:53:02,969] [INFO] Task started: Blastn
[2023-06-08 13:53:02,969] [INFO] Running command: blastn -query GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e0dd9b6-b8de-49ec-9fdc-482faa9b9ff2/dqc_reference/reference_markers_gtdb.fasta -out GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:53:03,571] [INFO] Task succeeded: Blastn
[2023-06-08 13:53:03,576] [INFO] Selected 12 target genomes.
[2023-06-08 13:53:03,576] [INFO] Target genome list was writen to GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:53:03,577] [INFO] Task started: fastANI
[2023-06-08 13:53:03,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e405b6-4553-499e-83aa-e84e2e674f8a/GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:53:09,944] [INFO] Task succeeded: fastANI
[2023-06-08 13:53:09,959] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:53:09,959] [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_900543975.1	s__Prevotella sp900543975	97.7459	303	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	conclusive
GCF_019052365.1	s__Prevotella sp000434975	78.2388	96	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_002265625.1	s__Prevotella sp002265625	77.6854	112	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_900553155.1	s__Prevotella sp900553155	77.5549	83	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCF_018789675.1	s__Prevotella sp002300055	77.5379	62	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCA_900544495.1	s__Prevotella sp900544495	77.5274	99	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900550035.1	s__Prevotella sp900550035	77.4688	95	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_900546575.1	s__Prevotella sp900546575	77.4251	87	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_900316285.1	s__Prevotella sp900316285	76.6722	55	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.02	95.37	0.87	0.79	21	-
GCF_900290275.1	s__Prevotella sp900290275	76.5921	74	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	-
--------------------------------------------------------------------------------
[2023-06-08 13:53:09,961] [INFO] GTDB search result was written to GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:53:09,961] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:53:09,964] [INFO] DFAST_QC result json was written to GCA_945486115.1_SRR7188235_bin.57_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:53:09,964] [INFO] DFAST_QC completed!
[2023-06-08 13:53:09,964] [INFO] Total running time: 0h0m52s