[2023-06-08 09:05:24,220] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:05:24,224] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:05:24,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d5e41cd-a817-422d-ad81-416a52390d8e/dqc_reference
[2023-06-08 09:05:25,599] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:05:25,600] [INFO] Task started: Prodigal
[2023-06-08 09:05:25,600] [INFO] Running command: gunzip -c /var/lib/cwl/stgab0475b5-eeaf-40c8-beb5-6b1d8ceee464/GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:05:38,236] [INFO] Task succeeded: Prodigal
[2023-06-08 09:05:38,236] [INFO] Task started: HMMsearch
[2023-06-08 09:05:38,236] [INFO] Running command: hmmsearch --tblout GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d5e41cd-a817-422d-ad81-416a52390d8e/dqc_reference/reference_markers.hmm GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:05:38,480] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:05:38,482] [INFO] Found 6/6 markers.
[2023-06-08 09:05:38,514] [INFO] Query marker FASTA was written to GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:05:38,515] [INFO] Task started: Blastn
[2023-06-08 09:05:38,515] [INFO] Running command: blastn -query GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5e41cd-a817-422d-ad81-416a52390d8e/dqc_reference/reference_markers.fasta -out GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:39,096] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:39,101] [INFO] Selected 30 target genomes.
[2023-06-08 09:05:39,102] [INFO] Target genome list was writen to GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:05:39,103] [INFO] Task started: fastANI
[2023-06-08 09:05:39,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgab0475b5-eeaf-40c8-beb5-6b1d8ceee464/GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:05:55,132] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:55,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d5e41cd-a817-422d-ad81-416a52390d8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:05:55,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d5e41cd-a817-422d-ad81-416a52390d8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:05:55,134] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:05:55,134] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:05:55,134] [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 09:05:55,143] [INFO] DFAST Taxonomy check result was written to GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:05:55,149] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:05:55,149] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:05:55,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d5e41cd-a817-422d-ad81-416a52390d8e/dqc_reference/checkm_data
[2023-06-08 09:05:55,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:05:55,183] [INFO] Task started: CheckM
[2023-06-08 09:05:55,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:06:35,435] [INFO] Task succeeded: CheckM
[2023-06-08 09:06:35,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:06:35,461] [INFO] ===== Completeness check finished =====
[2023-06-08 09:06:35,461] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:06:35,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:06:35,462] [INFO] Task started: Blastn
[2023-06-08 09:06:35,462] [INFO] Running command: blastn -query GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5e41cd-a817-422d-ad81-416a52390d8e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:06:36,270] [INFO] Task succeeded: Blastn
[2023-06-08 09:06:36,275] [INFO] Selected 28 target genomes.
[2023-06-08 09:06:36,275] [INFO] Target genome list was writen to GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:06:36,281] [INFO] Task started: fastANI
[2023-06-08 09:06:36,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgab0475b5-eeaf-40c8-beb5-6b1d8ceee464/GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:06:47,915] [INFO] Task succeeded: fastANI
[2023-06-08 09:06:47,931] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:06:47,931] [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_017503065.1	s__UBA4372 sp017503065	77.5388	111	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017547165.1	s__UBA4372 sp017547165	77.4391	74	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450165.1	s__UBA4372 sp002450165	77.3768	59	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.00	96.90	0.71	0.67	5	-
GCA_017558255.1	s__UBA4372 sp017558255	77.3096	61	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017381015.1	s__UBA4372 sp017381015	77.1631	64	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.60	97.07	0.87	0.84	3	-
GCA_017622815.1	s__UBA4372 sp017622815	76.9798	110	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.97	96.79	0.85	0.83	4	-
GCA_017628845.1	s__UBA4372 sp017628845	76.882	91	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469925.1	s__UBA4372 sp017469925	76.3873	52	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018064685.1	s__UBA4372 sp018064685	76.3196	80	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316355.1	s__UBA4372 sp900316355	76.2439	52	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.71	97.42	0.94	0.87	3	-
GCA_017524545.1	s__UBA4372 sp017524545	76.2431	76	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004559785.1	s__UBA4372 sp004559785	76.232	52	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935785.1	s__UBA4372 sp017935785	76.2227	57	697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.67	97.67	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-08 09:06:47,933] [INFO] GTDB search result was written to GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:06:47,934] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:06:47,937] [INFO] DFAST_QC result json was written to GCA_945831045.1_SRR5976182_bin.26_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:06:47,937] [INFO] DFAST_QC completed!
[2023-06-08 09:06:47,937] [INFO] Total running time: 0h1m24s