[2023-06-30 05:50:39,168] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:50:39,171] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:50:39,171] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4e78e48-644e-4470-beab-f22ec042aef7/dqc_reference
[2023-06-30 05:50:41,692] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:50:41,693] [INFO] Task started: Prodigal
[2023-06-30 05:50:41,693] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b91cf19-63da-4b22-907c-306fac815b8b/GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna.gz | prodigal -d GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/cds.fna -a GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:50:59,395] [INFO] Task succeeded: Prodigal
[2023-06-30 05:50:59,396] [INFO] Task started: HMMsearch
[2023-06-30 05:50:59,396] [INFO] Running command: hmmsearch --tblout GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4e78e48-644e-4470-beab-f22ec042aef7/dqc_reference/reference_markers.hmm GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:50:59,649] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:50:59,650] [INFO] Found 6/6 markers.
[2023-06-30 05:50:59,684] [INFO] Query marker FASTA was written to GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/markers.fasta
[2023-06-30 05:50:59,685] [INFO] Task started: Blastn
[2023-06-30 05:50:59,685] [INFO] Running command: blastn -query GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4e78e48-644e-4470-beab-f22ec042aef7/dqc_reference/reference_markers.fasta -out GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:51:00,290] [INFO] Task succeeded: Blastn
[2023-06-30 05:51:00,295] [INFO] Selected 21 target genomes.
[2023-06-30 05:51:00,296] [INFO] Target genome list was writen to GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/target_genomes.txt
[2023-06-30 05:51:00,304] [INFO] Task started: fastANI
[2023-06-30 05:51:00,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b91cf19-63da-4b22-907c-306fac815b8b/GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna.gz --refList GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/target_genomes.txt --output GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:51:13,710] [INFO] Task succeeded: fastANI
[2023-06-30 05:51:13,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4e78e48-644e-4470-beab-f22ec042aef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:51:13,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4e78e48-644e-4470-beab-f22ec042aef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:51:13,714] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:51:13,714] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:51:13,714] [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
--------------------------------------------------------------------------------
[2023-06-30 05:51:13,716] [INFO] DFAST Taxonomy check result was written to GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/tc_result.tsv
[2023-06-30 05:51:13,717] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:51:13,718] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:51:13,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4e78e48-644e-4470-beab-f22ec042aef7/dqc_reference/checkm_data
[2023-06-30 05:51:13,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:51:13,762] [INFO] Task started: CheckM
[2023-06-30 05:51:13,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/checkm_input GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/checkm_result
[2023-06-30 05:52:06,838] [INFO] Task succeeded: CheckM
[2023-06-30 05:52:06,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 05:52:06,862] [INFO] ===== Completeness check finished =====
[2023-06-30 05:52:06,862] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:52:06,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/markers.fasta)
[2023-06-30 05:52:06,863] [INFO] Task started: Blastn
[2023-06-30 05:52:06,863] [INFO] Running command: blastn -query GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4e78e48-644e-4470-beab-f22ec042aef7/dqc_reference/reference_markers_gtdb.fasta -out GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:52:07,722] [INFO] Task succeeded: Blastn
[2023-06-30 05:52:07,727] [INFO] Selected 14 target genomes.
[2023-06-30 05:52:07,728] [INFO] Target genome list was writen to GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:52:07,767] [INFO] Task started: fastANI
[2023-06-30 05:52:07,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b91cf19-63da-4b22-907c-306fac815b8b/GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna.gz --refList GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/target_genomes_gtdb.txt --output GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:52:16,464] [INFO] Task succeeded: fastANI
[2023-06-30 05:52:16,474] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:52:16,474] [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_903877385.1	s__CAIRDP01 sp903877385	99.9442	1125	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIRDP01	95.0	99.97	99.85	0.99	0.98	19	conclusive
GCA_903824935.1	s__CAIRDP01 sp903824935	79.8015	521	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIRDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887775.1	s__CAIRDP01 sp903887775	79.6581	602	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIRDP01	95.0	99.91	99.70	0.98	0.95	19	-
GCA_903837605.1	s__CAIRDP01 sp903837605	79.3247	593	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIRDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916595.1	s__CAIRDP01 sp903916595	78.0768	417	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIRDP01	95.0	99.47	99.16	0.88	0.85	24	-
GCA_009928665.1	s__SACF01 sp009928665	76.1436	52	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__SACF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882335.1	s__FEN-979 sp017882335	75.9781	55	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__FEN-979	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:52:16,476] [INFO] GTDB search result was written to GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/result_gtdb.tsv
[2023-06-30 05:52:16,477] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:52:16,480] [INFO] DFAST_QC result json was written to GCA_903821385.1_freshwater_MAG_---_MJ-time_bin-8768_genomic.fna/dqc_result.json
[2023-06-30 05:52:16,480] [INFO] DFAST_QC completed!
[2023-06-30 05:52:16,480] [INFO] Total running time: 0h1m37s