[2023-06-13 13:24:00,141] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:24:00,149] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:24:00,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b885e1f-94e4-45fe-a0cc-57cb6207b1ff/dqc_reference
[2023-06-13 13:24:01,917] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:24:01,918] [INFO] Task started: Prodigal
[2023-06-13 13:24:01,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg69fce901-912c-45ee-b4da-67960109e9f9/GCA_947449335.1_Jr-19feb18-13_genomic.fna.gz | prodigal -d GCA_947449335.1_Jr-19feb18-13_genomic.fna/cds.fna -a GCA_947449335.1_Jr-19feb18-13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:24:06,073] [INFO] Task succeeded: Prodigal
[2023-06-13 13:24:06,073] [INFO] Task started: HMMsearch
[2023-06-13 13:24:06,073] [INFO] Running command: hmmsearch --tblout GCA_947449335.1_Jr-19feb18-13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b885e1f-94e4-45fe-a0cc-57cb6207b1ff/dqc_reference/reference_markers.hmm GCA_947449335.1_Jr-19feb18-13_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:24:06,236] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:24:06,237] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg69fce901-912c-45ee-b4da-67960109e9f9/GCA_947449335.1_Jr-19feb18-13_genomic.fna.gz]
[2023-06-13 13:24:06,256] [INFO] Query marker FASTA was written to GCA_947449335.1_Jr-19feb18-13_genomic.fna/markers.fasta
[2023-06-13 13:24:06,256] [INFO] Task started: Blastn
[2023-06-13 13:24:06,256] [INFO] Running command: blastn -query GCA_947449335.1_Jr-19feb18-13_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b885e1f-94e4-45fe-a0cc-57cb6207b1ff/dqc_reference/reference_markers.fasta -out GCA_947449335.1_Jr-19feb18-13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:24:06,749] [INFO] Task succeeded: Blastn
[2023-06-13 13:24:06,753] [INFO] Selected 9 target genomes.
[2023-06-13 13:24:06,753] [INFO] Target genome list was writen to GCA_947449335.1_Jr-19feb18-13_genomic.fna/target_genomes.txt
[2023-06-13 13:24:06,754] [INFO] Task started: fastANI
[2023-06-13 13:24:06,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg69fce901-912c-45ee-b4da-67960109e9f9/GCA_947449335.1_Jr-19feb18-13_genomic.fna.gz --refList GCA_947449335.1_Jr-19feb18-13_genomic.fna/target_genomes.txt --output GCA_947449335.1_Jr-19feb18-13_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:24:11,760] [INFO] Task succeeded: fastANI
[2023-06-13 13:24:11,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b885e1f-94e4-45fe-a0cc-57cb6207b1ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:24:11,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b885e1f-94e4-45fe-a0cc-57cb6207b1ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:24:11,768] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:24:11,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:24:11,768] [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
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	78.1127	137	404	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.7952	150	404	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.7865	159	404	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.7519	127	404	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.7417	133	404	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	77.7183	135	404	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	77.6247	133	404	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	77.5873	132	404	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.3704	134	404	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:24:11,771] [INFO] DFAST Taxonomy check result was written to GCA_947449335.1_Jr-19feb18-13_genomic.fna/tc_result.tsv
[2023-06-13 13:24:11,771] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:24:11,771] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:24:11,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b885e1f-94e4-45fe-a0cc-57cb6207b1ff/dqc_reference/checkm_data
[2023-06-13 13:24:11,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:24:11,792] [INFO] Task started: CheckM
[2023-06-13 13:24:11,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947449335.1_Jr-19feb18-13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947449335.1_Jr-19feb18-13_genomic.fna/checkm_input GCA_947449335.1_Jr-19feb18-13_genomic.fna/checkm_result
[2023-06-13 13:24:29,359] [INFO] Task succeeded: CheckM
[2023-06-13 13:24:29,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 13:24:29,380] [INFO] ===== Completeness check finished =====
[2023-06-13 13:24:29,380] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:24:29,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947449335.1_Jr-19feb18-13_genomic.fna/markers.fasta)
[2023-06-13 13:24:29,381] [INFO] Task started: Blastn
[2023-06-13 13:24:29,381] [INFO] Running command: blastn -query GCA_947449335.1_Jr-19feb18-13_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b885e1f-94e4-45fe-a0cc-57cb6207b1ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_947449335.1_Jr-19feb18-13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:24:29,940] [INFO] Task succeeded: Blastn
[2023-06-13 13:24:29,943] [INFO] Selected 10 target genomes.
[2023-06-13 13:24:29,943] [INFO] Target genome list was writen to GCA_947449335.1_Jr-19feb18-13_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:24:29,944] [INFO] Task started: fastANI
[2023-06-13 13:24:29,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg69fce901-912c-45ee-b4da-67960109e9f9/GCA_947449335.1_Jr-19feb18-13_genomic.fna.gz --refList GCA_947449335.1_Jr-19feb18-13_genomic.fna/target_genomes_gtdb.txt --output GCA_947449335.1_Jr-19feb18-13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:24:36,818] [INFO] Task succeeded: fastANI
[2023-06-13 13:24:36,827] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:24:36,827] [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_002454975.1	s__Hylemonella sp002454975	77.965	141	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886275.1	s__Rhodoferax sp903886275	77.8404	147	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.88	99.42	0.96	0.95	10	-
GCF_003415675.1	s__Rhodoferax sp003415675	77.7865	159	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943465.1	s__Rhodoferax sp002943465	77.7186	158	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955715.1	s__Rhodoferax saidenbachensis	77.5873	132	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.99	99.99	1.00	1.00	2	-
GCA_017848645.1	s__Limnohabitans_A sp017848645	77.5518	145	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCA_903863395.1	s__Rhodoferax sp903863395	77.396	122	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.94	98.87	0.83	0.81	5	-
GCA_016719405.1	s__Rhodoferax sp016719405	77.3006	124	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.38	98.38	0.86	0.86	2	-
GCA_903845935.1	s__Rhodoferax sp903845935	77.2354	132	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.58	99.41	0.92	0.88	22	-
GCA_001770935.1	s__Rhodoferax sp001770935	77.1978	127	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:24:36,829] [INFO] GTDB search result was written to GCA_947449335.1_Jr-19feb18-13_genomic.fna/result_gtdb.tsv
[2023-06-13 13:24:36,830] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:24:36,833] [INFO] DFAST_QC result json was written to GCA_947449335.1_Jr-19feb18-13_genomic.fna/dqc_result.json
[2023-06-13 13:24:36,833] [INFO] DFAST_QC completed!
[2023-06-13 13:24:36,833] [INFO] Total running time: 0h0m37s