[2023-06-08 12:31:39,807] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:31:39,810] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:31:39,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgcecb3655-204e-4c51-9a68-a16dfbe0f2ef/dqc_reference
[2023-06-08 12:31:41,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:31:41,150] [INFO] Task started: Prodigal
[2023-06-08 12:31:41,150] [INFO] Running command: gunzip -c /var/lib/cwl/stgb312ea5e-e30a-431f-bca6-e177ee3fcf50/GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:31:45,571] [INFO] Task succeeded: Prodigal
[2023-06-08 12:31:45,571] [INFO] Task started: HMMsearch
[2023-06-08 12:31:45,571] [INFO] Running command: hmmsearch --tblout GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcecb3655-204e-4c51-9a68-a16dfbe0f2ef/dqc_reference/reference_markers.hmm GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:31:45,800] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:31:45,801] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb312ea5e-e30a-431f-bca6-e177ee3fcf50/GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 12:31:45,826] [INFO] Query marker FASTA was written to GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:31:45,826] [INFO] Task started: Blastn
[2023-06-08 12:31:45,827] [INFO] Running command: blastn -query GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecb3655-204e-4c51-9a68-a16dfbe0f2ef/dqc_reference/reference_markers.fasta -out GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:31:46,393] [INFO] Task succeeded: Blastn
[2023-06-08 12:31:46,396] [INFO] Selected 16 target genomes.
[2023-06-08 12:31:46,397] [INFO] Target genome list was writen to GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:31:46,400] [INFO] Task started: fastANI
[2023-06-08 12:31:46,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgb312ea5e-e30a-431f-bca6-e177ee3fcf50/GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:31:55,168] [INFO] Task succeeded: fastANI
[2023-06-08 12:31:55,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcecb3655-204e-4c51-9a68-a16dfbe0f2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:31:55,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcecb3655-204e-4c51-9a68-a16dfbe0f2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:31:55,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:31:55,172] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:31:55,172] [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 12:31:55,174] [INFO] DFAST Taxonomy check result was written to GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:31:55,175] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:31:55,175] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:31:55,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcecb3655-204e-4c51-9a68-a16dfbe0f2ef/dqc_reference/checkm_data
[2023-06-08 12:31:55,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:31:55,204] [INFO] Task started: CheckM
[2023-06-08 12:31:55,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:32:15,107] [INFO] Task succeeded: CheckM
[2023-06-08 12:32:15,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:32:15,128] [INFO] ===== Completeness check finished =====
[2023-06-08 12:32:15,129] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:32:15,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:32:15,129] [INFO] Task started: Blastn
[2023-06-08 12:32:15,130] [INFO] Running command: blastn -query GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecb3655-204e-4c51-9a68-a16dfbe0f2ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:32:15,898] [INFO] Task succeeded: Blastn
[2023-06-08 12:32:15,903] [INFO] Selected 9 target genomes.
[2023-06-08 12:32:15,903] [INFO] Target genome list was writen to GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:32:15,909] [INFO] Task started: fastANI
[2023-06-08 12:32:15,910] [INFO] Running command: fastANI --query /var/lib/cwl/stgb312ea5e-e30a-431f-bca6-e177ee3fcf50/GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:32:19,209] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:19,222] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:32:19,222] [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_004555265.1	s__Fimenecus sp004555265	97.6184	400	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	97.83	97.21	0.88	0.84	3	conclusive
GCA_900766945.1	s__Fimenecus sp900766945	91.2261	297	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540295.1	s__Fimenecus sp900540295	79.0628	208	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.52	98.30	0.90	0.86	3	-
GCA_018712805.1	s__Fimenecus excrementavium	79.0534	193	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.06	98.06	0.85	0.85	2	-
GCA_002490525.1	s__Fimenecus sp002490525	78.2584	181	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	99.95	99.94	0.93	0.88	4	-
GCA_002314305.1	s__Fimenecus stercoravium	77.9577	111	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	97.83	97.74	0.77	0.75	3	-
GCA_900545625.1	s__Fimenecus sp900545625	77.508	143	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432435.1	s__Fimenecus sp000432435	76.7826	50	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.55	98.08	0.94	0.85	30	-
--------------------------------------------------------------------------------
[2023-06-08 12:32:19,224] [INFO] GTDB search result was written to GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:32:19,225] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:32:19,229] [INFO] DFAST_QC result json was written to GCA_945877795.1_ERR1855546_bin.24_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:32:19,229] [INFO] DFAST_QC completed!
[2023-06-08 12:32:19,229] [INFO] Total running time: 0h0m39s