[2023-06-07 23:37:48,013] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:37:48,016] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:37:48,016] [INFO] DQC Reference Directory: /var/lib/cwl/stge17fa640-c185-4325-af77-b2393c99f136/dqc_reference
[2023-06-07 23:37:49,361] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:37:49,362] [INFO] Task started: Prodigal
[2023-06-07 23:37:49,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg865d5947-5d2a-4621-b930-0e3ffeb04c7b/GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:38:01,254] [INFO] Task succeeded: Prodigal
[2023-06-07 23:38:01,255] [INFO] Task started: HMMsearch
[2023-06-07 23:38:01,255] [INFO] Running command: hmmsearch --tblout GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge17fa640-c185-4325-af77-b2393c99f136/dqc_reference/reference_markers.hmm GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:38:01,493] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:38:01,495] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg865d5947-5d2a-4621-b930-0e3ffeb04c7b/GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 23:38:01,517] [INFO] Query marker FASTA was written to GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 23:38:01,518] [INFO] Task started: Blastn
[2023-06-07 23:38:01,518] [INFO] Running command: blastn -query GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge17fa640-c185-4325-af77-b2393c99f136/dqc_reference/reference_markers.fasta -out GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:38:02,121] [INFO] Task succeeded: Blastn
[2023-06-07 23:38:02,124] [INFO] Selected 22 target genomes.
[2023-06-07 23:38:02,125] [INFO] Target genome list was writen to GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 23:38:02,126] [INFO] Task started: fastANI
[2023-06-07 23:38:02,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg865d5947-5d2a-4621-b930-0e3ffeb04c7b/GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:38:13,685] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:13,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge17fa640-c185-4325-af77-b2393c99f136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:38:13,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge17fa640-c185-4325-af77-b2393c99f136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:38:13,689] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:38:13,689] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 23:38:13,689] [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
--------------------------------------------------------------------------------
[2023-06-07 23:38:13,692] [INFO] DFAST Taxonomy check result was written to GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 23:38:13,692] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:38:13,693] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:38:13,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge17fa640-c185-4325-af77-b2393c99f136/dqc_reference/checkm_data
[2023-06-07 23:38:13,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:38:13,721] [INFO] Task started: CheckM
[2023-06-07 23:38:13,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 23:38:50,845] [INFO] Task succeeded: CheckM
[2023-06-07 23:38:50,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:38:50,869] [INFO] ===== Completeness check finished =====
[2023-06-07 23:38:50,869] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:38:50,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 23:38:50,870] [INFO] Task started: Blastn
[2023-06-07 23:38:50,870] [INFO] Running command: blastn -query GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge17fa640-c185-4325-af77-b2393c99f136/dqc_reference/reference_markers_gtdb.fasta -out GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:38:51,799] [INFO] Task succeeded: Blastn
[2023-06-07 23:38:51,803] [INFO] Selected 19 target genomes.
[2023-06-07 23:38:51,803] [INFO] Target genome list was writen to GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:38:51,805] [INFO] Task started: fastANI
[2023-06-07 23:38:51,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg865d5947-5d2a-4621-b930-0e3ffeb04c7b/GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:38:59,883] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:59,898] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 23:38:59,899] [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_018064685.1	s__UBA4372 sp018064685	79.1048	228	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065005.1	s__UBA4372 sp018065005	77.609	123	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017503065.1	s__UBA4372 sp017503065	77.424	85	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292545.1	s__UBA4372 sp016292545	77.3427	118	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543815.1	s__UBA4372 sp900543815	76.9736	93	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.82	97.58	0.92	0.88	4	-
GCA_905234735.1	s__UBA4372 sp905234735	76.9682	88	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017444005.1	s__UBA4372 sp017444005	76.9324	108	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017379075.1	s__UBA4372 sp017379075	76.8103	68	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.81	95.71	0.83	0.83	3	-
GCA_902783655.1	s__UBA4372 sp902783655	76.7954	82	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395775.1	s__UBA4372 sp002395775	76.7806	97	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.87	96.87	0.81	0.81	2	-
GCA_017470425.1	s__UBA4372 sp017470425	76.6812	69	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.15	97.15	0.50	0.50	2	-
GCA_902768105.1	s__Prevotella sp902768105	76.428	51	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128475.1	s__Bacteroides massiliensis	76.3126	55	517	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
--------------------------------------------------------------------------------
[2023-06-07 23:38:59,900] [INFO] GTDB search result was written to GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 23:38:59,901] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:38:59,903] [INFO] DFAST_QC result json was written to GCA_945827435.1_SRR5976180_bin.27_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 23:38:59,904] [INFO] DFAST_QC completed!
[2023-06-07 23:38:59,904] [INFO] Total running time: 0h1m12s