[2023-06-08 12:26:29,784] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:29,787] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:29,787] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4ee73f2-d371-4bdd-a836-cf8e08b4ec2f/dqc_reference
[2023-06-08 12:26:31,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:31,083] [INFO] Task started: Prodigal
[2023-06-08 12:26:31,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg07fd09e6-b0b8-4ec1-a5af-1cc740b6b0fc/GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:44,147] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:44,147] [INFO] Task started: HMMsearch
[2023-06-08 12:26:44,147] [INFO] Running command: hmmsearch --tblout GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4ee73f2-d371-4bdd-a836-cf8e08b4ec2f/dqc_reference/reference_markers.hmm GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:44,414] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:44,416] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg07fd09e6-b0b8-4ec1-a5af-1cc740b6b0fc/GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 12:26:44,444] [INFO] Query marker FASTA was written to GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:26:44,444] [INFO] Task started: Blastn
[2023-06-08 12:26:44,444] [INFO] Running command: blastn -query GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ee73f2-d371-4bdd-a836-cf8e08b4ec2f/dqc_reference/reference_markers.fasta -out GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:45,170] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:45,174] [INFO] Selected 15 target genomes.
[2023-06-08 12:26:45,174] [INFO] Target genome list was writen to GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:26:45,179] [INFO] Task started: fastANI
[2023-06-08 12:26:45,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg07fd09e6-b0b8-4ec1-a5af-1cc740b6b0fc/GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:26:56,687] [INFO] Task succeeded: fastANI
[2023-06-08 12:26:56,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4ee73f2-d371-4bdd-a836-cf8e08b4ec2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:26:56,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4ee73f2-d371-4bdd-a836-cf8e08b4ec2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:26:56,690] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:26:56,690] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:26:56,690] [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
--------------------------------------------------------------------------------
[2023-06-08 12:26:56,696] [INFO] DFAST Taxonomy check result was written to GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:26:56,697] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:26:56,697] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:26:56,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4ee73f2-d371-4bdd-a836-cf8e08b4ec2f/dqc_reference/checkm_data
[2023-06-08 12:26:56,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:26:56,730] [INFO] Task started: CheckM
[2023-06-08 12:26:56,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:27:40,225] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:40,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 9.47%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:40,259] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:40,260] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:40,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:27:40,261] [INFO] Task started: Blastn
[2023-06-08 12:27:40,261] [INFO] Running command: blastn -query GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ee73f2-d371-4bdd-a836-cf8e08b4ec2f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:41,215] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:41,219] [INFO] Selected 13 target genomes.
[2023-06-08 12:27:41,219] [INFO] Target genome list was writen to GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:41,222] [INFO] Task started: fastANI
[2023-06-08 12:27:41,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg07fd09e6-b0b8-4ec1-a5af-1cc740b6b0fc/GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:46,881] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:46,892] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:27:46,893] [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_000434935.1	s__Cryptobacteroides sp000434935	96.8188	623	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.20	96.88	0.85	0.83	4	conclusive
GCA_000432515.1	s__Cryptobacteroides sp000432515	82.0381	347	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.23	97.18	0.82	0.82	4	-
GCA_000435075.1	s__Cryptobacteroides sp000435075	81.293	331	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.30	97.06	0.87	0.85	4	-
GCA_900546925.1	s__Cryptobacteroides sp900546925	79.8493	223	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.81	98.70	0.85	0.79	6	-
GCA_004552615.1	s__Cryptobacteroides sp004552615	77.844	148	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.38	98.38	0.80	0.80	2	-
GCA_900769145.1	s__Cryptobacteroides sp900769145	77.7221	139	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694885.1	s__Cryptobacteroides faecipullorum	77.4809	53	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	77.1281	94	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
GCA_015060385.1	s__Cryptobacteroides sp015060385	76.3467	51	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319855.1	s__Cryptobacteroides sp900319855	76.0239	56	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.60	97.81	0.89	0.84	6	-
GCA_017483985.1	s__Cryptobacteroides sp017483985	75.8065	55	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317925.1	s__Cryptobacteroides sp900317925	75.6669	50	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	96.11	0.85	0.74	52	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:46,895] [INFO] GTDB search result was written to GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:46,896] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:46,899] [INFO] DFAST_QC result json was written to GCA_945932635.1_SRR11489790_bin.10_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:27:46,900] [INFO] DFAST_QC completed!
[2023-06-08 12:27:46,900] [INFO] Total running time: 0h1m17s