[2023-06-30 11:36:37,598] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:36:37,602] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:36:37,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg1285f169-a530-4e3c-84aa-769e221de519/dqc_reference
[2023-06-30 11:36:39,087] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:36:39,088] [INFO] Task started: Prodigal
[2023-06-30 11:36:39,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg87da6337-7325-422c-a4c1-7d559bdde3e3/GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna.gz | prodigal -d GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/cds.fna -a GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:36:48,584] [INFO] Task succeeded: Prodigal
[2023-06-30 11:36:48,584] [INFO] Task started: HMMsearch
[2023-06-30 11:36:48,584] [INFO] Running command: hmmsearch --tblout GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1285f169-a530-4e3c-84aa-769e221de519/dqc_reference/reference_markers.hmm GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:36:48,774] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:36:48,775] [INFO] Found 6/6 markers.
[2023-06-30 11:36:48,804] [INFO] Query marker FASTA was written to GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/markers.fasta
[2023-06-30 11:36:48,805] [INFO] Task started: Blastn
[2023-06-30 11:36:48,805] [INFO] Running command: blastn -query GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/markers.fasta -db /var/lib/cwl/stg1285f169-a530-4e3c-84aa-769e221de519/dqc_reference/reference_markers.fasta -out GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:36:49,365] [INFO] Task succeeded: Blastn
[2023-06-30 11:36:49,369] [INFO] Selected 23 target genomes.
[2023-06-30 11:36:49,369] [INFO] Target genome list was writen to GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/target_genomes.txt
[2023-06-30 11:36:49,371] [INFO] Task started: fastANI
[2023-06-30 11:36:49,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg87da6337-7325-422c-a4c1-7d559bdde3e3/GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna.gz --refList GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/target_genomes.txt --output GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:37:03,784] [INFO] Task succeeded: fastANI
[2023-06-30 11:37:03,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1285f169-a530-4e3c-84aa-769e221de519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:37:03,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1285f169-a530-4e3c-84aa-769e221de519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:37:03,786] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:37:03,786] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 11:37:03,786] [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 11:37:03,788] [INFO] DFAST Taxonomy check result was written to GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/tc_result.tsv
[2023-06-30 11:37:03,788] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:37:03,788] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:37:03,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1285f169-a530-4e3c-84aa-769e221de519/dqc_reference/checkm_data
[2023-06-30 11:37:03,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:37:03,826] [INFO] Task started: CheckM
[2023-06-30 11:37:03,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/checkm_input GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/checkm_result
[2023-06-30 11:37:34,842] [INFO] Task succeeded: CheckM
[2023-06-30 11:37:34,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:37:34,860] [INFO] ===== Completeness check finished =====
[2023-06-30 11:37:34,861] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:37:34,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/markers.fasta)
[2023-06-30 11:37:34,861] [INFO] Task started: Blastn
[2023-06-30 11:37:34,861] [INFO] Running command: blastn -query GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/markers.fasta -db /var/lib/cwl/stg1285f169-a530-4e3c-84aa-769e221de519/dqc_reference/reference_markers_gtdb.fasta -out GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:37:35,750] [INFO] Task succeeded: Blastn
[2023-06-30 11:37:35,753] [INFO] Selected 17 target genomes.
[2023-06-30 11:37:35,753] [INFO] Target genome list was writen to GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:37:35,758] [INFO] Task started: fastANI
[2023-06-30 11:37:35,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg87da6337-7325-422c-a4c1-7d559bdde3e3/GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna.gz --refList GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/target_genomes_gtdb.txt --output GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:37:47,201] [INFO] Task succeeded: fastANI
[2023-06-30 11:37:47,208] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:37:47,209] [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_903829565.1	s__SXXH01 sp903829565	100.0	750	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SXXH01	95.0	98.11	97.95	0.77	0.75	5	conclusive
GCA_005789645.1	s__SXXH01 sp005789645	78.9731	334	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SXXH01	95.0	99.62	99.60	0.89	0.88	4	-
GCA_016709875.1	s__JADJLZ01 sp016709875	77.3576	145	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	77.3351	149	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795245.1	s__JAEUIA01 sp016795245	77.0195	142	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUIA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	76.9236	137	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220035.1	s__JADJNY01 sp016220035	76.8719	105	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.7252	87	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928115.1	s__F1-120-MAGs118 sp903928115	76.6395	107	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.83	99.80	0.95	0.95	3	-
GCA_007751475.1	s__GCA-2862085 sp007751475	76.0288	52	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	75.4957	53	762	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 11:37:47,210] [INFO] GTDB search result was written to GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/result_gtdb.tsv
[2023-06-30 11:37:47,211] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:37:47,214] [INFO] DFAST_QC result json was written to GCA_903829565.1_freshwater_MAG_---_Erken-D8_bin-0018_genomic.fna/dqc_result.json
[2023-06-30 11:37:47,214] [INFO] DFAST_QC completed!
[2023-06-30 11:37:47,214] [INFO] Total running time: 0h1m10s