[2023-07-01 04:39:32,755] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:39:32,758] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:39:32,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg9597d37b-0f1d-46f3-9fcd-2632ae1de4e8/dqc_reference
[2023-07-01 04:39:33,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:39:33,947] [INFO] Task started: Prodigal
[2023-07-01 04:39:33,947] [INFO] Running command: gunzip -c /var/lib/cwl/stga6429c7f-ae7c-4f54-a97f-163de013e3e9/GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna.gz | prodigal -d GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/cds.fna -a GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:39:53,283] [INFO] Task succeeded: Prodigal
[2023-07-01 04:39:53,284] [INFO] Task started: HMMsearch
[2023-07-01 04:39:53,284] [INFO] Running command: hmmsearch --tblout GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9597d37b-0f1d-46f3-9fcd-2632ae1de4e8/dqc_reference/reference_markers.hmm GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:39:53,526] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:39:53,528] [INFO] Found 6/6 markers.
[2023-07-01 04:39:53,568] [INFO] Query marker FASTA was written to GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/markers.fasta
[2023-07-01 04:39:53,569] [INFO] Task started: Blastn
[2023-07-01 04:39:53,569] [INFO] Running command: blastn -query GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/markers.fasta -db /var/lib/cwl/stg9597d37b-0f1d-46f3-9fcd-2632ae1de4e8/dqc_reference/reference_markers.fasta -out GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:39:54,150] [INFO] Task succeeded: Blastn
[2023-07-01 04:39:54,154] [INFO] Selected 32 target genomes.
[2023-07-01 04:39:54,155] [INFO] Target genome list was writen to GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/target_genomes.txt
[2023-07-01 04:39:54,156] [INFO] Task started: fastANI
[2023-07-01 04:39:54,156] [INFO] Running command: fastANI --query /var/lib/cwl/stga6429c7f-ae7c-4f54-a97f-163de013e3e9/GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna.gz --refList GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/target_genomes.txt --output GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:40:12,906] [INFO] Task succeeded: fastANI
[2023-07-01 04:40:12,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9597d37b-0f1d-46f3-9fcd-2632ae1de4e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:40:12,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9597d37b-0f1d-46f3-9fcd-2632ae1de4e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:40:12,908] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:40:12,908] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:40:12,908] [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
--------------------------------------------------------------------------------
[2023-07-01 04:40:12,910] [INFO] DFAST Taxonomy check result was written to GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/tc_result.tsv
[2023-07-01 04:40:12,910] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:40:12,910] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:40:12,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9597d37b-0f1d-46f3-9fcd-2632ae1de4e8/dqc_reference/checkm_data
[2023-07-01 04:40:12,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:40:12,963] [INFO] Task started: CheckM
[2023-07-01 04:40:12,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/checkm_input GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/checkm_result
[2023-07-01 04:41:08,443] [INFO] Task succeeded: CheckM
[2023-07-01 04:41:08,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:41:08,460] [INFO] ===== Completeness check finished =====
[2023-07-01 04:41:08,461] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:41:08,461] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/markers.fasta)
[2023-07-01 04:41:08,461] [INFO] Task started: Blastn
[2023-07-01 04:41:08,461] [INFO] Running command: blastn -query GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/markers.fasta -db /var/lib/cwl/stg9597d37b-0f1d-46f3-9fcd-2632ae1de4e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:41:09,238] [INFO] Task succeeded: Blastn
[2023-07-01 04:41:09,241] [INFO] Selected 20 target genomes.
[2023-07-01 04:41:09,241] [INFO] Target genome list was writen to GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:41:09,242] [INFO] Task started: fastANI
[2023-07-01 04:41:09,242] [INFO] Running command: fastANI --query /var/lib/cwl/stga6429c7f-ae7c-4f54-a97f-163de013e3e9/GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna.gz --refList GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/target_genomes_gtdb.txt --output GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:41:21,778] [INFO] Task succeeded: fastANI
[2023-07-01 04:41:21,790] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:41:21,790] [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_903847205.1	s__2-12-FULL-35-15 sp903847205	100.0	1793	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_003151815.1	s__2-12-FULL-35-15 sp003151815	77.0435	181	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001769385.1	s__2-12-FULL-35-15 sp001769385	76.9824	283	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919535.1	s__2-12-FULL-35-15 sp903919535	76.7563	230	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.81	99.81	0.93	0.93	2	-
GCA_903870175.1	s__2-12-FULL-35-15 sp903870175	76.5918	137	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.44	99.36	0.89	0.82	6	-
GCA_903881065.1	s__2-12-FULL-35-15 sp903881065	76.4515	138	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786925.1	s__JAEUTT01 sp016786925	76.2543	116	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787165.1	s__JAEUTT01 sp016787165	76.0757	98	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303895.1	s__JAEUTT01 sp017303895	76.0277	124	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903833025.1	s__2-12-FULL-35-15 sp903833025	75.9212	103	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903923915.1	s__PALSA-968 sp903923915	75.4838	53	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__PALSA-968	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153315.1	s__PALSA-968 sp003153315	75.3521	76	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__PALSA-968	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709575.1	s__JAFLBH01 sp016709575	75.1629	59	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 04:41:21,792] [INFO] GTDB search result was written to GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/result_gtdb.tsv
[2023-07-01 04:41:21,792] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:41:21,795] [INFO] DFAST_QC result json was written to GCA_903847205.1_freshwater_MAG_---_Kiruna_bin-09443_genomic.fna/dqc_result.json
[2023-07-01 04:41:21,795] [INFO] DFAST_QC completed!
[2023-07-01 04:41:21,795] [INFO] Total running time: 0h1m49s