[2023-06-30 12:52:45,822] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:52:45,833] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:52:45,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg0692b8ce-7342-4b59-8b42-383758d8b43d/dqc_reference
[2023-06-30 12:52:47,363] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:52:47,364] [INFO] Task started: Prodigal
[2023-06-30 12:52:47,365] [INFO] Running command: gunzip -c /var/lib/cwl/stg47155a59-1f27-4ffb-a867-e872d0ce21c5/GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna.gz | prodigal -d GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/cds.fna -a GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:52:58,621] [INFO] Task succeeded: Prodigal
[2023-06-30 12:52:58,622] [INFO] Task started: HMMsearch
[2023-06-30 12:52:58,622] [INFO] Running command: hmmsearch --tblout GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0692b8ce-7342-4b59-8b42-383758d8b43d/dqc_reference/reference_markers.hmm GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:52:58,912] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:52:58,914] [INFO] Found 6/6 markers.
[2023-06-30 12:52:58,959] [INFO] Query marker FASTA was written to GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/markers.fasta
[2023-06-30 12:52:58,960] [INFO] Task started: Blastn
[2023-06-30 12:52:58,960] [INFO] Running command: blastn -query GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/markers.fasta -db /var/lib/cwl/stg0692b8ce-7342-4b59-8b42-383758d8b43d/dqc_reference/reference_markers.fasta -out GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:52:59,693] [INFO] Task succeeded: Blastn
[2023-06-30 12:52:59,697] [INFO] Selected 19 target genomes.
[2023-06-30 12:52:59,697] [INFO] Target genome list was writen to GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/target_genomes.txt
[2023-06-30 12:52:59,698] [INFO] Task started: fastANI
[2023-06-30 12:52:59,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg47155a59-1f27-4ffb-a867-e872d0ce21c5/GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna.gz --refList GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/target_genomes.txt --output GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:53:15,382] [INFO] Task succeeded: fastANI
[2023-06-30 12:53:15,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0692b8ce-7342-4b59-8b42-383758d8b43d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:53:15,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0692b8ce-7342-4b59-8b42-383758d8b43d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:53:15,397] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:53:15,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:53:15,398] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	83.9389	688	1211	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	77.9398	296	1211	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	75.8703	81	1211	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.6886	68	1211	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	75.6574	87	1211	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	75.596	94	1211	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	75.548	78	1211	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.5291	70	1211	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	75.2914	108	1211	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.2559	124	1211	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.1771	134	1211	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.1689	127	1211	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	75.0098	103	1211	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	74.9549	100	1211	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	74.8958	77	1211	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:53:15,400] [INFO] DFAST Taxonomy check result was written to GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/tc_result.tsv
[2023-06-30 12:53:15,401] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:53:15,402] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:53:15,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0692b8ce-7342-4b59-8b42-383758d8b43d/dqc_reference/checkm_data
[2023-06-30 12:53:15,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:53:15,446] [INFO] Task started: CheckM
[2023-06-30 12:53:15,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/checkm_input GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/checkm_result
[2023-06-30 12:53:51,099] [INFO] Task succeeded: CheckM
[2023-06-30 12:53:51,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 12:53:51,123] [INFO] ===== Completeness check finished =====
[2023-06-30 12:53:51,124] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:53:51,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/markers.fasta)
[2023-06-30 12:53:51,125] [INFO] Task started: Blastn
[2023-06-30 12:53:51,125] [INFO] Running command: blastn -query GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/markers.fasta -db /var/lib/cwl/stg0692b8ce-7342-4b59-8b42-383758d8b43d/dqc_reference/reference_markers_gtdb.fasta -out GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:53:52,293] [INFO] Task succeeded: Blastn
[2023-06-30 12:53:52,298] [INFO] Selected 7 target genomes.
[2023-06-30 12:53:52,298] [INFO] Target genome list was writen to GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:53:52,299] [INFO] Task started: fastANI
[2023-06-30 12:53:52,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg47155a59-1f27-4ffb-a867-e872d0ce21c5/GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna.gz --refList GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/target_genomes_gtdb.txt --output GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:53:58,237] [INFO] Task succeeded: fastANI
[2023-06-30 12:53:58,249] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:53:58,249] [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_903937385.1	s__Geothrix sp903937385	99.902	1135	1211	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.84	98.90	0.96	0.91	10	conclusive
GCA_903857495.1	s__Geothrix sp903857495	93.7248	1000	1211	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.99	99.97	0.99	0.98	50	-
GCA_903863195.1	s__Geothrix sp903863195	92.5891	873	1211	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_013334395.1	s__Geothrix sp013334395	91.7963	767	1211	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843705.1	s__Geothrix sp903843705	90.1719	854	1211	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	-
GCA_903876615.1	s__Geothrix sp903876615	90.0002	520	1211	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903890595.1	s__Geothrix sp903890595	84.5674	602	1211	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.18	98.75	0.85	0.81	6	-
--------------------------------------------------------------------------------
[2023-06-30 12:53:58,251] [INFO] GTDB search result was written to GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/result_gtdb.tsv
[2023-06-30 12:53:58,252] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:53:58,255] [INFO] DFAST_QC result json was written to GCA_903893685.1_freshwater_MAG_---_D14_bin-0990_genomic.fna/dqc_result.json
[2023-06-30 12:53:58,255] [INFO] DFAST_QC completed!
[2023-06-30 12:53:58,256] [INFO] Total running time: 0h1m12s