[2023-06-29 09:02:34,225] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:34,254] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:34,254] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f30ddee-348f-4d70-ac27-f57b6f61579b/dqc_reference
[2023-06-29 09:02:35,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:35,614] [INFO] Task started: Prodigal
[2023-06-29 09:02:35,614] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7ce2de8-356b-457f-9210-a90174653efa/GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:47,888] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:47,888] [INFO] Task started: HMMsearch
[2023-06-29 09:02:47,888] [INFO] Running command: hmmsearch --tblout GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f30ddee-348f-4d70-ac27-f57b6f61579b/dqc_reference/reference_markers.hmm GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:48,146] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:48,148] [INFO] Found 6/6 markers.
[2023-06-29 09:02:48,172] [INFO] Query marker FASTA was written to GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 09:02:48,172] [INFO] Task started: Blastn
[2023-06-29 09:02:48,173] [INFO] Running command: blastn -query GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f30ddee-348f-4d70-ac27-f57b6f61579b/dqc_reference/reference_markers.fasta -out GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:48,775] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:48,779] [INFO] Selected 35 target genomes.
[2023-06-29 09:02:48,779] [INFO] Target genome list was writen to GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 09:02:48,785] [INFO] Task started: fastANI
[2023-06-29 09:02:48,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ce2de8-356b-457f-9210-a90174653efa/GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:03:15,468] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:15,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f30ddee-348f-4d70-ac27-f57b6f61579b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:03:15,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f30ddee-348f-4d70-ac27-f57b6f61579b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:03:15,471] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:03:15,471] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 09:03:15,471] [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
--------------------------------------------------------------------------------
[2023-06-29 09:03:15,474] [INFO] DFAST Taxonomy check result was written to GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 09:03:15,474] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:03:15,475] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:03:15,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f30ddee-348f-4d70-ac27-f57b6f61579b/dqc_reference/checkm_data
[2023-06-29 09:03:15,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:03:15,503] [INFO] Task started: CheckM
[2023-06-29 09:03:15,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 09:03:52,867] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:52,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:52,889] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:52,889] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:52,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 09:03:52,890] [INFO] Task started: Blastn
[2023-06-29 09:03:52,890] [INFO] Running command: blastn -query GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f30ddee-348f-4d70-ac27-f57b6f61579b/dqc_reference/reference_markers_gtdb.fasta -out GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:53,749] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:53,754] [INFO] Selected 16 target genomes.
[2023-06-29 09:03:53,755] [INFO] Target genome list was writen to GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:53,760] [INFO] Task started: fastANI
[2023-06-29 09:03:53,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ce2de8-356b-457f-9210-a90174653efa/GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:04:01,425] [INFO] Task succeeded: fastANI
[2023-06-29 09:04:01,443] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 09:04:01,443] [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_900541925.1	s__Cryptobacteroides sp900541925	97.8809	613	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.89	97.86	0.90	0.88	3	conclusive
GCA_002438805.1	s__Cryptobacteroides sp002438805	83.2716	500	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.44	99.33	0.95	0.94	4	-
GCA_002439095.1	s__Cryptobacteroides sp002439095	83.173	503	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.02	98.66	0.95	0.93	5	-
GCA_900769905.1	s__Cryptobacteroides sp900769905	79.0595	172	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.32	0.78	0.78	2	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	78.5987	191	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_017477245.1	s__Cryptobacteroides sp017477245	78.5901	220	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	-
GCA_017454905.1	s__Cryptobacteroides sp017454905	78.2763	220	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543205.1	s__Cryptobacteroides excrementigallinarum	78.2684	189	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.70	97.70	0.89	0.89	2	-
GCA_018715685.1	s__Cryptobacteroides merdipullorum	78.2579	194	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234475.1	s__Cryptobacteroides sp905234475	78.208	172	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790635.1	s__Cryptobacteroides sp902790635	78.2028	182	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555145.1	s__Cryptobacteroides sp004555145	78.1844	125	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535125.1	s__Cryptobacteroides sp017535125	78.0852	160	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780175.1	s__Cryptobacteroides sp902780175	77.7166	91	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.78	95.78	0.73	0.73	2	-
GCA_017551425.1	s__Cryptobacteroides sp017551425	77.4378	88	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471045.1	s__Cryptobacteroides sp017471045	77.1207	100	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:04:01,445] [INFO] GTDB search result was written to GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 09:04:01,446] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:04:01,449] [INFO] DFAST_QC result json was written to GCA_948468845.1_SRR17622768_bin.50_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 09:04:01,449] [INFO] DFAST_QC completed!
[2023-06-29 09:04:01,449] [INFO] Total running time: 0h1m27s