[2023-06-30 00:55:17,079] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:55:17,081] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:55:17,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg98feb7dd-184c-48ea-99b1-4a186426f058/dqc_reference
[2023-06-30 00:55:18,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:55:18,548] [INFO] Task started: Prodigal
[2023-06-30 00:55:18,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d7bfc55-7166-4db8-9043-9161dbb4595c/GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna.gz | prodigal -d GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/cds.fna -a GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:55:48,190] [INFO] Task succeeded: Prodigal
[2023-06-30 00:55:48,190] [INFO] Task started: HMMsearch
[2023-06-30 00:55:48,190] [INFO] Running command: hmmsearch --tblout GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98feb7dd-184c-48ea-99b1-4a186426f058/dqc_reference/reference_markers.hmm GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:55:48,486] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:55:48,487] [INFO] Found 6/6 markers.
[2023-06-30 00:55:48,533] [INFO] Query marker FASTA was written to GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/markers.fasta
[2023-06-30 00:55:48,534] [INFO] Task started: Blastn
[2023-06-30 00:55:48,534] [INFO] Running command: blastn -query GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/markers.fasta -db /var/lib/cwl/stg98feb7dd-184c-48ea-99b1-4a186426f058/dqc_reference/reference_markers.fasta -out GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:55:49,191] [INFO] Task succeeded: Blastn
[2023-06-30 00:55:49,197] [INFO] Selected 16 target genomes.
[2023-06-30 00:55:49,198] [INFO] Target genome list was writen to GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/target_genomes.txt
[2023-06-30 00:55:49,200] [INFO] Task started: fastANI
[2023-06-30 00:55:49,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d7bfc55-7166-4db8-9043-9161dbb4595c/GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna.gz --refList GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/target_genomes.txt --output GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:56:02,223] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:02,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98feb7dd-184c-48ea-99b1-4a186426f058/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:56:02,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98feb7dd-184c-48ea-99b1-4a186426f058/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:56:02,230] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:56:02,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:56:02,231] [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
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.6099	175	1351	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.5571	176	1351	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.7095	57	1351	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.6681	56	1351	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	75.1401	52	1351	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:56:02,233] [INFO] DFAST Taxonomy check result was written to GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/tc_result.tsv
[2023-06-30 00:56:02,233] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:56:02,233] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:56:02,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98feb7dd-184c-48ea-99b1-4a186426f058/dqc_reference/checkm_data
[2023-06-30 00:56:02,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:56:02,285] [INFO] Task started: CheckM
[2023-06-30 00:56:02,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/checkm_input GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/checkm_result
[2023-06-30 00:57:22,281] [INFO] Task succeeded: CheckM
[2023-06-30 00:57:22,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:57:22,304] [INFO] ===== Completeness check finished =====
[2023-06-30 00:57:22,304] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:57:22,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/markers.fasta)
[2023-06-30 00:57:22,305] [INFO] Task started: Blastn
[2023-06-30 00:57:22,305] [INFO] Running command: blastn -query GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/markers.fasta -db /var/lib/cwl/stg98feb7dd-184c-48ea-99b1-4a186426f058/dqc_reference/reference_markers_gtdb.fasta -out GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:57:23,131] [INFO] Task succeeded: Blastn
[2023-06-30 00:57:23,136] [INFO] Selected 13 target genomes.
[2023-06-30 00:57:23,136] [INFO] Target genome list was writen to GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:57:23,139] [INFO] Task started: fastANI
[2023-06-30 00:57:23,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d7bfc55-7166-4db8-9043-9161dbb4595c/GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna.gz --refList GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/target_genomes_gtdb.txt --output GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:57:33,818] [INFO] Task succeeded: fastANI
[2023-06-30 00:57:33,831] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:57:33,832] [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_903929475.1	s__SXWH01 sp903929475	99.881	1269	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	99.90	99.90	0.94	0.94	2	conclusive
GCA_014189875.1	s__SXWH01 sp014189875	79.1486	374	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882875.1	s__SXWH01 sp903882875	78.8265	448	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	99.98	99.97	0.98	0.98	3	-
GCA_903874975.1	s__Chthoniobacter sp903874975	77.5986	243	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	97.99	97.82	0.84	0.83	3	-
GCA_005791535.1	s__SXWH01 sp005791535	77.2002	223	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885995.1	s__VFJQ01 sp009885995	77.1694	263	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__VFJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173075.1	s__Chthoniobacter flavus	76.6325	173	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	99.97	99.97	0.99	0.99	2	-
GCA_018970255.1	s__UBA967 sp018970255	76.037	64	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901425.1	s__CAIURC01 sp903901425	75.6856	54	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__CAIURC01	95.0	99.87	99.80	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2023-06-30 00:57:33,834] [INFO] GTDB search result was written to GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/result_gtdb.tsv
[2023-06-30 00:57:33,834] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:57:33,838] [INFO] DFAST_QC result json was written to GCA_903834585.1_freshwater_MAG_---_Umea1_bin-3045_genomic.fna/dqc_result.json
[2023-06-30 00:57:33,838] [INFO] DFAST_QC completed!
[2023-06-30 00:57:33,838] [INFO] Total running time: 0h2m17s