[2023-06-29 22:16:50,657] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:16:50,659] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:16:50,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg414772fe-2c63-4356-9363-32bb1816532b/dqc_reference
[2023-06-29 22:16:51,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:16:51,824] [INFO] Task started: Prodigal
[2023-06-29 22:16:51,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e8a32af-0b6a-4f6c-b7c1-946cf217d101/GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna.gz | prodigal -d GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/cds.fna -a GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:17:13,881] [INFO] Task succeeded: Prodigal
[2023-06-29 22:17:13,882] [INFO] Task started: HMMsearch
[2023-06-29 22:17:13,882] [INFO] Running command: hmmsearch --tblout GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg414772fe-2c63-4356-9363-32bb1816532b/dqc_reference/reference_markers.hmm GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:17:14,163] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:17:14,164] [INFO] Found 6/6 markers.
[2023-06-29 22:17:14,199] [INFO] Query marker FASTA was written to GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/markers.fasta
[2023-06-29 22:17:14,200] [INFO] Task started: Blastn
[2023-06-29 22:17:14,200] [INFO] Running command: blastn -query GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/markers.fasta -db /var/lib/cwl/stg414772fe-2c63-4356-9363-32bb1816532b/dqc_reference/reference_markers.fasta -out GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:17:14,783] [INFO] Task succeeded: Blastn
[2023-06-29 22:17:14,787] [INFO] Selected 31 target genomes.
[2023-06-29 22:17:14,788] [INFO] Target genome list was writen to GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/target_genomes.txt
[2023-06-29 22:17:14,793] [INFO] Task started: fastANI
[2023-06-29 22:17:14,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e8a32af-0b6a-4f6c-b7c1-946cf217d101/GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna.gz --refList GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/target_genomes.txt --output GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:17:38,093] [INFO] Task succeeded: fastANI
[2023-06-29 22:17:38,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg414772fe-2c63-4356-9363-32bb1816532b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:17:38,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg414772fe-2c63-4356-9363-32bb1816532b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:17:38,096] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:17:38,096] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:17:38,096] [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 22:17:38,098] [INFO] DFAST Taxonomy check result was written to GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/tc_result.tsv
[2023-06-29 22:17:38,099] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:17:38,099] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:17:38,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg414772fe-2c63-4356-9363-32bb1816532b/dqc_reference/checkm_data
[2023-06-29 22:17:38,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:17:38,149] [INFO] Task started: CheckM
[2023-06-29 22:17:38,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/checkm_input GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/checkm_result
[2023-06-29 22:18:43,451] [INFO] Task succeeded: CheckM
[2023-06-29 22:18:43,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:18:43,474] [INFO] ===== Completeness check finished =====
[2023-06-29 22:18:43,474] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:18:43,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/markers.fasta)
[2023-06-29 22:18:43,475] [INFO] Task started: Blastn
[2023-06-29 22:18:43,475] [INFO] Running command: blastn -query GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/markers.fasta -db /var/lib/cwl/stg414772fe-2c63-4356-9363-32bb1816532b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:18:44,261] [INFO] Task succeeded: Blastn
[2023-06-29 22:18:44,266] [INFO] Selected 20 target genomes.
[2023-06-29 22:18:44,266] [INFO] Target genome list was writen to GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:18:44,278] [INFO] Task started: fastANI
[2023-06-29 22:18:44,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e8a32af-0b6a-4f6c-b7c1-946cf217d101/GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna.gz --refList GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/target_genomes_gtdb.txt --output GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:19:00,629] [INFO] Task succeeded: fastANI
[2023-06-29 22:19:00,642] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:19:00,642] [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_903836265.1	s__M3007 sp903836265	99.4755	1057	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	99.54	99.41	0.90	0.87	7	conclusive
GCA_903925535.1	s__M3007 sp903925535	82.5727	771	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903933805.1	s__M3007 sp903933805	76.6409	69	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	99.57	99.51	0.91	0.90	6	-
GCA_016787415.1	s__M3007 sp016787415	76.348	87	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331955.1	s__M3007 sp011331955	76.3146	64	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187225.1	s__M3007 sp019187225	76.2086	91	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303875.1	s__M3007 sp017303875	76.1954	71	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787545.1	s__M3007 sp016787545	76.0888	64	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303475.1	s__M3007 sp017303475	75.9251	81	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712415.1	s__M3007 sp016712415	75.887	83	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711435.1	s__M3007 sp016711435	75.8467	93	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708875.1	s__M3007 sp016708875	75.7599	68	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787285.1	s__M3007 sp016787285	75.667	67	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719605.1	s__M3007 sp016719605	75.5946	66	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716135.1	s__M3007 sp016716135	75.4906	50	1280	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:19:00,644] [INFO] GTDB search result was written to GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/result_gtdb.tsv
[2023-06-29 22:19:00,645] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:19:00,648] [INFO] DFAST_QC result json was written to GCA_903866405.1_freshwater_MAG_---_LaPlata-b_bin-2048_genomic.fna/dqc_result.json
[2023-06-29 22:19:00,648] [INFO] DFAST_QC completed!
[2023-06-29 22:19:00,648] [INFO] Total running time: 0h2m10s