[2023-06-08 19:44:11,325] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:44:11,327] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:44:11,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f1fff90-9e8e-47d9-8ac9-647f5307dd98/dqc_reference
[2023-06-08 19:44:12,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:44:12,532] [INFO] Task started: Prodigal
[2023-06-08 19:44:12,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfe33bc4-ad20-4453-be2c-f7a453cc818e/GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:44:20,860] [INFO] Task succeeded: Prodigal
[2023-06-08 19:44:20,861] [INFO] Task started: HMMsearch
[2023-06-08 19:44:20,861] [INFO] Running command: hmmsearch --tblout GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f1fff90-9e8e-47d9-8ac9-647f5307dd98/dqc_reference/reference_markers.hmm GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:44:21,091] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:44:21,092] [INFO] Found 6/6 markers.
[2023-06-08 19:44:21,112] [INFO] Query marker FASTA was written to GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:44:21,112] [INFO] Task started: Blastn
[2023-06-08 19:44:21,112] [INFO] Running command: blastn -query GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1fff90-9e8e-47d9-8ac9-647f5307dd98/dqc_reference/reference_markers.fasta -out GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:44:21,675] [INFO] Task succeeded: Blastn
[2023-06-08 19:44:21,680] [INFO] Selected 25 target genomes.
[2023-06-08 19:44:21,681] [INFO] Target genome list was writen to GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:44:21,685] [INFO] Task started: fastANI
[2023-06-08 19:44:21,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe33bc4-ad20-4453-be2c-f7a453cc818e/GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:44:37,841] [INFO] Task succeeded: fastANI
[2023-06-08 19:44:37,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f1fff90-9e8e-47d9-8ac9-647f5307dd98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:44:37,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f1fff90-9e8e-47d9-8ac9-647f5307dd98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:44:37,843] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:44:37,844] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 19:44:37,844] [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 19:44:37,846] [INFO] DFAST Taxonomy check result was written to GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:44:37,846] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:44:37,847] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:44:37,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f1fff90-9e8e-47d9-8ac9-647f5307dd98/dqc_reference/checkm_data
[2023-06-08 19:44:37,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:44:37,872] [INFO] Task started: CheckM
[2023-06-08 19:44:37,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:45:07,201] [INFO] Task succeeded: CheckM
[2023-06-08 19:45:07,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:45:07,223] [INFO] ===== Completeness check finished =====
[2023-06-08 19:45:07,223] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:45:07,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:45:07,224] [INFO] Task started: Blastn
[2023-06-08 19:45:07,224] [INFO] Running command: blastn -query GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1fff90-9e8e-47d9-8ac9-647f5307dd98/dqc_reference/reference_markers_gtdb.fasta -out GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:45:08,018] [INFO] Task succeeded: Blastn
[2023-06-08 19:45:08,024] [INFO] Selected 31 target genomes.
[2023-06-08 19:45:08,024] [INFO] Target genome list was writen to GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:45:08,032] [INFO] Task started: fastANI
[2023-06-08 19:45:08,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe33bc4-ad20-4453-be2c-f7a453cc818e/GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:45:18,147] [INFO] Task succeeded: fastANI
[2023-06-08 19:45:18,168] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 19:45:18,168] [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_900769905.1	s__Cryptobacteroides sp900769905	79.2044	88	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.32	0.78	0.78	2	-
GCA_900541925.1	s__Cryptobacteroides sp900541925	77.5856	61	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.89	97.86	0.90	0.88	3	-
GCA_016286145.1	s__Cryptobacteroides sp016286145	77.4113	77	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.77	98.72	0.82	0.81	3	-
GCA_016295245.1	s__Cryptobacteroides sp016295245	77.3265	67	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.61	98.61	0.79	0.79	2	-
GCA_905234775.1	s__Cryptobacteroides sp905234775	77.2506	83	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538685.1	s__Cryptobacteroides sp017538685	77.1546	68	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287875.1	s__Cryptobacteroides sp016287875	77.1516	67	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	77.1145	57	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_905234485.1	s__Cryptobacteroides sp905234485	77.1145	84	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.26	99.26	0.82	0.82	2	-
GCA_004555145.1	s__Cryptobacteroides sp004555145	77.1057	64	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900771005.1	s__Cryptobacteroides sp900771005	77.098	52	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066125.1	s__Cryptobacteroides sp018066125	77.0775	59	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617035.1	s__Cryptobacteroides sp017617035	77.0527	81	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769145.1	s__Cryptobacteroides sp900769145	76.9924	59	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615435.1	s__Cryptobacteroides sp017615435	76.9621	87	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	76.9594	56	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_017455065.1	s__Cryptobacteroides sp017455065	76.8561	69	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	76.7737	59	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	76.7632	61	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_017620335.1	s__Cryptobacteroides sp017620335	76.5984	62	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:45:18,170] [INFO] GTDB search result was written to GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:45:18,171] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:45:18,175] [INFO] DFAST_QC result json was written to GCA_945836735.1_SRR5666654_bin.33_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:45:18,175] [INFO] DFAST_QC completed!
[2023-06-08 19:45:18,175] [INFO] Total running time: 0h1m7s