[2023-06-28 07:34:11,295] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:34:11,298] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:34:11,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg7360ae50-0316-445d-810c-fab50ba9f163/dqc_reference
[2023-06-28 07:34:12,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:34:12,526] [INFO] Task started: Prodigal
[2023-06-28 07:34:12,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f4b2373-16c0-4de3-9d2a-9965b0127491/GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:34:17,235] [INFO] Task succeeded: Prodigal
[2023-06-28 07:34:17,236] [INFO] Task started: HMMsearch
[2023-06-28 07:34:17,236] [INFO] Running command: hmmsearch --tblout GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7360ae50-0316-445d-810c-fab50ba9f163/dqc_reference/reference_markers.hmm GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:34:17,456] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:34:17,457] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f4b2373-16c0-4de3-9d2a-9965b0127491/GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 07:34:17,480] [INFO] Query marker FASTA was written to GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 07:34:17,481] [INFO] Task started: Blastn
[2023-06-28 07:34:17,481] [INFO] Running command: blastn -query GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7360ae50-0316-445d-810c-fab50ba9f163/dqc_reference/reference_markers.fasta -out GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:34:18,056] [INFO] Task succeeded: Blastn
[2023-06-28 07:34:18,061] [INFO] Selected 25 target genomes.
[2023-06-28 07:34:18,061] [INFO] Target genome list was writen to GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 07:34:18,066] [INFO] Task started: fastANI
[2023-06-28 07:34:18,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4b2373-16c0-4de3-9d2a-9965b0127491/GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:34:28,777] [INFO] Task succeeded: fastANI
[2023-06-28 07:34:28,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7360ae50-0316-445d-810c-fab50ba9f163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:34:28,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7360ae50-0316-445d-810c-fab50ba9f163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:34:28,780] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:34:28,780] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 07:34:28,780] [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
--------------------------------------------------------------------------------
[2023-06-28 07:34:28,783] [INFO] DFAST Taxonomy check result was written to GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 07:34:28,783] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:34:28,784] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:34:28,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7360ae50-0316-445d-810c-fab50ba9f163/dqc_reference/checkm_data
[2023-06-28 07:34:28,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:34:28,812] [INFO] Task started: CheckM
[2023-06-28 07:34:28,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 07:34:50,574] [INFO] Task succeeded: CheckM
[2023-06-28 07:34:50,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 6.19%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:34:50,602] [INFO] ===== Completeness check finished =====
[2023-06-28 07:34:50,603] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:34:50,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 07:34:50,603] [INFO] Task started: Blastn
[2023-06-28 07:34:50,604] [INFO] Running command: blastn -query GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7360ae50-0316-445d-810c-fab50ba9f163/dqc_reference/reference_markers_gtdb.fasta -out GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:34:51,402] [INFO] Task succeeded: Blastn
[2023-06-28 07:34:51,407] [INFO] Selected 23 target genomes.
[2023-06-28 07:34:51,407] [INFO] Target genome list was writen to GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:34:51,422] [INFO] Task started: fastANI
[2023-06-28 07:34:51,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4b2373-16c0-4de3-9d2a-9965b0127491/GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:34:57,799] [INFO] Task succeeded: fastANI
[2023-06-28 07:34:57,814] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 07:34:57,814] [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_002696275.1	s__GCA-002697625 sp002696275	99.8643	482	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002697625.1	s__GCA-002697625 sp002697625	80.4542	312	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478555.1	s__GCA-002697625 sp905478555	78.1845	206	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_902514225.1	s__GCA-002697625 sp902514225	77.8947	126	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647945.1	s__GCA-002697625 sp018647945	77.706	175	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
GCA_018695965.1	s__GCA-002697625 sp018695965	77.6772	167	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	98.45	97.65	0.78	0.72	6	-
GCA_018664745.1	s__UWMA-0277 sp018664745	76.6368	64	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579065.1	s__GCA-002715885 sp902579065	76.5979	59	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.5859	95	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381465.1	s__DUAL01 sp014381465	76.3954	85	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711125.1	s__GCA-2711125 sp002711125	75.9571	86	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_018675825.1	s__GCA-002715885 sp018675825	75.9248	57	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:34:57,816] [INFO] GTDB search result was written to GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 07:34:57,817] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:34:57,820] [INFO] DFAST_QC result json was written to GCA_913052035.1_ERR599012_bin.6_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 07:34:57,820] [INFO] DFAST_QC completed!
[2023-06-28 07:34:57,820] [INFO] Total running time: 0h0m47s