[2023-06-27 13:54:43,970] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:54:43,974] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:54:43,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f48c898-b224-4583-bd3d-012564f447a5/dqc_reference
[2023-06-27 13:54:45,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:54:45,185] [INFO] Task started: Prodigal
[2023-06-27 13:54:45,185] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa5329f7-d088-44a8-bc60-b165b3129d20/GCA_026399565.1_ASM2639956v1_genomic.fna.gz | prodigal -d GCA_026399565.1_ASM2639956v1_genomic.fna/cds.fna -a GCA_026399565.1_ASM2639956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:54:53,453] [INFO] Task succeeded: Prodigal
[2023-06-27 13:54:53,454] [INFO] Task started: HMMsearch
[2023-06-27 13:54:53,454] [INFO] Running command: hmmsearch --tblout GCA_026399565.1_ASM2639956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f48c898-b224-4583-bd3d-012564f447a5/dqc_reference/reference_markers.hmm GCA_026399565.1_ASM2639956v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:54:53,654] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:54:53,655] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfa5329f7-d088-44a8-bc60-b165b3129d20/GCA_026399565.1_ASM2639956v1_genomic.fna.gz]
[2023-06-27 13:54:53,687] [INFO] Query marker FASTA was written to GCA_026399565.1_ASM2639956v1_genomic.fna/markers.fasta
[2023-06-27 13:54:53,688] [INFO] Task started: Blastn
[2023-06-27 13:54:53,688] [INFO] Running command: blastn -query GCA_026399565.1_ASM2639956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f48c898-b224-4583-bd3d-012564f447a5/dqc_reference/reference_markers.fasta -out GCA_026399565.1_ASM2639956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:54:54,251] [INFO] Task succeeded: Blastn
[2023-06-27 13:54:54,255] [INFO] Selected 16 target genomes.
[2023-06-27 13:54:54,255] [INFO] Target genome list was writen to GCA_026399565.1_ASM2639956v1_genomic.fna/target_genomes.txt
[2023-06-27 13:54:54,256] [INFO] Task started: fastANI
[2023-06-27 13:54:54,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa5329f7-d088-44a8-bc60-b165b3129d20/GCA_026399565.1_ASM2639956v1_genomic.fna.gz --refList GCA_026399565.1_ASM2639956v1_genomic.fna/target_genomes.txt --output GCA_026399565.1_ASM2639956v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:55:03,030] [INFO] Task succeeded: fastANI
[2023-06-27 13:55:03,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f48c898-b224-4583-bd3d-012564f447a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:55:03,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f48c898-b224-4583-bd3d-012564f447a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:55:03,040] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 13:55:03,040] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 13:55:03,040] [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
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	78.2203	124	693	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	78.1579	152	693	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.1395	153	693	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	77.0019	102	693	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	76.9521	104	693	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	76.8185	85	693	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	76.6665	101	693	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.5273	74	693	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.4928	109	693	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	75.4502	74	693	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 13:55:03,042] [INFO] DFAST Taxonomy check result was written to GCA_026399565.1_ASM2639956v1_genomic.fna/tc_result.tsv
[2023-06-27 13:55:03,043] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:55:03,043] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:55:03,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f48c898-b224-4583-bd3d-012564f447a5/dqc_reference/checkm_data
[2023-06-27 13:55:03,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:55:03,079] [INFO] Task started: CheckM
[2023-06-27 13:55:03,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026399565.1_ASM2639956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026399565.1_ASM2639956v1_genomic.fna/checkm_input GCA_026399565.1_ASM2639956v1_genomic.fna/checkm_result
[2023-06-27 13:55:31,110] [INFO] Task succeeded: CheckM
[2023-06-27 13:55:31,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.90%
Contamintation: 1.77%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 13:55:31,130] [INFO] ===== Completeness check finished =====
[2023-06-27 13:55:31,130] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:55:31,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026399565.1_ASM2639956v1_genomic.fna/markers.fasta)
[2023-06-27 13:55:31,131] [INFO] Task started: Blastn
[2023-06-27 13:55:31,131] [INFO] Running command: blastn -query GCA_026399565.1_ASM2639956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f48c898-b224-4583-bd3d-012564f447a5/dqc_reference/reference_markers_gtdb.fasta -out GCA_026399565.1_ASM2639956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:55:31,780] [INFO] Task succeeded: Blastn
[2023-06-27 13:55:31,784] [INFO] Selected 18 target genomes.
[2023-06-27 13:55:31,784] [INFO] Target genome list was writen to GCA_026399565.1_ASM2639956v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:55:31,790] [INFO] Task started: fastANI
[2023-06-27 13:55:31,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa5329f7-d088-44a8-bc60-b165b3129d20/GCA_026399565.1_ASM2639956v1_genomic.fna.gz --refList GCA_026399565.1_ASM2639956v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026399565.1_ASM2639956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:55:42,908] [INFO] Task succeeded: fastANI
[2023-06-27 13:55:42,920] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 13:55:42,920] [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_016234745.1	s__JACRAR01 sp016234745	82.3876	408	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016194935.1	s__JACRAR01 sp016194935	79.501	205	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900174485.1	s__Sterolibacterium denitrificans	78.365	157	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sterolibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832735.1	s__CAIYYX01 sp903832735	78.3214	194	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAIYYX01	95.0	99.74	99.50	0.95	0.91	27	-
GCF_003865015.1	s__Sulfurisoma sediminicola	78.1161	154	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
GCA_903904605.1	s__CAIYYX01 sp903904605	77.96	207	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAIYYX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930535.1	s__CAIYYX01 sp903930535	77.6453	166	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAIYYX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016880655.1	s__Fen-999 sp016880655	77.427	104	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330945.1	s__UBA2250 sp011330945	77.1595	132	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	99.90	99.90	0.95	0.95	2	-
GCA_018062105.1	s__Sterolibacterium sp018062105	77.0196	86	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sterolibacterium	95.0	99.77	99.77	0.89	0.89	2	-
GCA_018828385.1	s__Azonexus sp018828385	76.666	83	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	100.00	100.00	1.00	1.00	4	-
GCF_004345725.1	s__Crenobacter luteus	76.5273	74	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCA_017302315.1	s__Zoogloea sp017302315	76.1276	80	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307915.1	s__SCN-69-89 sp017307915	75.9664	82	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 13:55:42,922] [INFO] GTDB search result was written to GCA_026399565.1_ASM2639956v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:55:42,923] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:55:42,926] [INFO] DFAST_QC result json was written to GCA_026399565.1_ASM2639956v1_genomic.fna/dqc_result.json
[2023-06-27 13:55:42,926] [INFO] DFAST_QC completed!
[2023-06-27 13:55:42,927] [INFO] Total running time: 0h0m59s