[2023-06-08 14:09:36,733] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:09:36,736] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:09:36,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c0261cf-34c6-4b97-90c6-12a592e47a80/dqc_reference
[2023-06-08 14:09:38,029] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:09:38,030] [INFO] Task started: Prodigal
[2023-06-08 14:09:38,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e11c382-f21b-4bcd-8910-b9f95c458b22/GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:09:49,987] [INFO] Task succeeded: Prodigal
[2023-06-08 14:09:49,987] [INFO] Task started: HMMsearch
[2023-06-08 14:09:49,988] [INFO] Running command: hmmsearch --tblout GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c0261cf-34c6-4b97-90c6-12a592e47a80/dqc_reference/reference_markers.hmm GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:09:50,267] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:09:50,268] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3e11c382-f21b-4bcd-8910-b9f95c458b22/GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 14:09:50,291] [INFO] Query marker FASTA was written to GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 14:09:50,292] [INFO] Task started: Blastn
[2023-06-08 14:09:50,292] [INFO] Running command: blastn -query GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c0261cf-34c6-4b97-90c6-12a592e47a80/dqc_reference/reference_markers.fasta -out GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:09:50,916] [INFO] Task succeeded: Blastn
[2023-06-08 14:09:50,919] [INFO] Selected 19 target genomes.
[2023-06-08 14:09:50,920] [INFO] Target genome list was writen to GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:09:50,923] [INFO] Task started: fastANI
[2023-06-08 14:09:50,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e11c382-f21b-4bcd-8910-b9f95c458b22/GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:10:01,405] [INFO] Task succeeded: fastANI
[2023-06-08 14:10:01,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c0261cf-34c6-4b97-90c6-12a592e47a80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:10:01,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c0261cf-34c6-4b97-90c6-12a592e47a80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:10:01,412] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:10:01,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:10:01,412] [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
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	77.6141	58	602	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.6467	57	602	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.1761	54	602	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.167	53	602	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:10:01,415] [INFO] DFAST Taxonomy check result was written to GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:10:01,415] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:10:01,416] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:10:01,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c0261cf-34c6-4b97-90c6-12a592e47a80/dqc_reference/checkm_data
[2023-06-08 14:10:01,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:10:01,450] [INFO] Task started: CheckM
[2023-06-08 14:10:01,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 14:10:39,451] [INFO] Task succeeded: CheckM
[2023-06-08 14:10:39,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 3.65%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-08 14:10:39,476] [INFO] ===== Completeness check finished =====
[2023-06-08 14:10:39,476] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:10:39,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:10:39,477] [INFO] Task started: Blastn
[2023-06-08 14:10:39,477] [INFO] Running command: blastn -query GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c0261cf-34c6-4b97-90c6-12a592e47a80/dqc_reference/reference_markers_gtdb.fasta -out GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:10:40,358] [INFO] Task succeeded: Blastn
[2023-06-08 14:10:40,363] [INFO] Selected 19 target genomes.
[2023-06-08 14:10:40,363] [INFO] Target genome list was writen to GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:10:40,374] [INFO] Task started: fastANI
[2023-06-08 14:10:40,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e11c382-f21b-4bcd-8910-b9f95c458b22/GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:10:47,980] [INFO] Task succeeded: fastANI
[2023-06-08 14:10:48,005] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:10:48,005] [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_002373375.1	s__Prevotella sp002373375	95.4155	433	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.88	95.14	0.78	0.66	9	conclusive
GCA_002392645.1	s__Prevotella sp002392645	82.6497	219	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.38	96.38	0.66	0.66	2	-
GCA_016281055.1	s__Prevotella sp016281055	80.1848	249	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017413085.1	s__Prevotella sp017413085	80.0756	212	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	98.36	0.87	0.87	2	-
GCA_017642485.1	s__Prevotella sp017642485	78.3788	91	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233245.1	s__Prevotella sp905233245	78.2627	98	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.81	0.80	0.79	3	-
GCA_002353585.1	s__Prevotella sp002353585	78.0117	117	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.91	95.27	0.85	0.76	8	-
GCA_017479675.1	s__Prevotella sp017479675	77.908	93	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.13	0.63	0.60	3	-
GCA_905233165.1	s__Prevotella sp905233165	77.8579	77	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478025.1	s__Prevotella sp017478025	77.7311	106	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.24	95.24	0.74	0.74	2	-
GCA_902774795.1	s__Prevotella sp902774795	77.6533	89	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475005.1	s__Prevotella sp017475005	77.6283	76	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.77	0.88	0.88	2	-
GCA_017623655.1	s__Prevotella sp017623655	77.6268	74	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013166595.1	s__Prevotella sp002298815	77.6141	58	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.88	99.76	0.99	0.99	4	-
GCA_017541365.1	s__Prevotella sp017541365	77.5651	97	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353975.1	s__Prevotella sp002353975	77.271	85	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.48	0.79	0.75	4	-
GCA_018065145.1	s__Prevotella sp018065145	77.2221	102	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:10:48,007] [INFO] GTDB search result was written to GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:10:48,008] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:10:48,011] [INFO] DFAST_QC result json was written to GCA_945828895.1_SRR5240726_bin.23_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:10:48,011] [INFO] DFAST_QC completed!
[2023-06-08 14:10:48,011] [INFO] Total running time: 0h1m11s