[2023-06-08 14:18:29,105] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:18:29,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:18:29,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg7061fcf4-9a42-401c-9069-6abf56b9951d/dqc_reference
[2023-06-08 14:18:30,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:18:30,302] [INFO] Task started: Prodigal
[2023-06-08 14:18:30,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg6885fead-30a7-4533-8503-d1336dedff86/GCA_947445095.1_Jr-08jan18-31_genomic.fna.gz | prodigal -d GCA_947445095.1_Jr-08jan18-31_genomic.fna/cds.fna -a GCA_947445095.1_Jr-08jan18-31_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:18:37,348] [INFO] Task succeeded: Prodigal
[2023-06-08 14:18:37,349] [INFO] Task started: HMMsearch
[2023-06-08 14:18:37,349] [INFO] Running command: hmmsearch --tblout GCA_947445095.1_Jr-08jan18-31_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7061fcf4-9a42-401c-9069-6abf56b9951d/dqc_reference/reference_markers.hmm GCA_947445095.1_Jr-08jan18-31_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:18:37,537] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:18:37,539] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6885fead-30a7-4533-8503-d1336dedff86/GCA_947445095.1_Jr-08jan18-31_genomic.fna.gz]
[2023-06-08 14:18:37,566] [INFO] Query marker FASTA was written to GCA_947445095.1_Jr-08jan18-31_genomic.fna/markers.fasta
[2023-06-08 14:18:37,566] [INFO] Task started: Blastn
[2023-06-08 14:18:37,566] [INFO] Running command: blastn -query GCA_947445095.1_Jr-08jan18-31_genomic.fna/markers.fasta -db /var/lib/cwl/stg7061fcf4-9a42-401c-9069-6abf56b9951d/dqc_reference/reference_markers.fasta -out GCA_947445095.1_Jr-08jan18-31_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:18:38,059] [INFO] Task succeeded: Blastn
[2023-06-08 14:18:38,064] [INFO] Selected 18 target genomes.
[2023-06-08 14:18:38,064] [INFO] Target genome list was writen to GCA_947445095.1_Jr-08jan18-31_genomic.fna/target_genomes.txt
[2023-06-08 14:18:38,068] [INFO] Task started: fastANI
[2023-06-08 14:18:38,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg6885fead-30a7-4533-8503-d1336dedff86/GCA_947445095.1_Jr-08jan18-31_genomic.fna.gz --refList GCA_947445095.1_Jr-08jan18-31_genomic.fna/target_genomes.txt --output GCA_947445095.1_Jr-08jan18-31_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:18:49,742] [INFO] Task succeeded: fastANI
[2023-06-08 14:18:49,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7061fcf4-9a42-401c-9069-6abf56b9951d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:18:49,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7061fcf4-9a42-401c-9069-6abf56b9951d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:18:49,759] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:18:49,759] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:18:49,759] [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
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	77.9743	224	677	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	77.9736	231	677	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	77.83	240	677	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.1527	145	677	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.9029	144	677	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.8292	139	677	95	below_threshold
Polaromonas vacuolata	strain=KCTC 22033	GCA_012584515.1	37448	37448	type	True	76.7796	131	677	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	76.6926	100	677	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	76.5112	148	677	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	76.2127	131	677	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.0594	67	677	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:18:49,762] [INFO] DFAST Taxonomy check result was written to GCA_947445095.1_Jr-08jan18-31_genomic.fna/tc_result.tsv
[2023-06-08 14:18:49,762] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:18:49,762] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:18:49,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7061fcf4-9a42-401c-9069-6abf56b9951d/dqc_reference/checkm_data
[2023-06-08 14:18:49,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:18:49,793] [INFO] Task started: CheckM
[2023-06-08 14:18:49,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947445095.1_Jr-08jan18-31_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947445095.1_Jr-08jan18-31_genomic.fna/checkm_input GCA_947445095.1_Jr-08jan18-31_genomic.fna/checkm_result
[2023-06-08 14:19:16,092] [INFO] Task succeeded: CheckM
[2023-06-08 14:19:16,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:19:16,114] [INFO] ===== Completeness check finished =====
[2023-06-08 14:19:16,114] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:19:16,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947445095.1_Jr-08jan18-31_genomic.fna/markers.fasta)
[2023-06-08 14:19:16,115] [INFO] Task started: Blastn
[2023-06-08 14:19:16,115] [INFO] Running command: blastn -query GCA_947445095.1_Jr-08jan18-31_genomic.fna/markers.fasta -db /var/lib/cwl/stg7061fcf4-9a42-401c-9069-6abf56b9951d/dqc_reference/reference_markers_gtdb.fasta -out GCA_947445095.1_Jr-08jan18-31_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:19:16,628] [INFO] Task succeeded: Blastn
[2023-06-08 14:19:16,632] [INFO] Selected 14 target genomes.
[2023-06-08 14:19:16,632] [INFO] Target genome list was writen to GCA_947445095.1_Jr-08jan18-31_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:19:16,640] [INFO] Task started: fastANI
[2023-06-08 14:19:16,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg6885fead-30a7-4533-8503-d1336dedff86/GCA_947445095.1_Jr-08jan18-31_genomic.fna.gz --refList GCA_947445095.1_Jr-08jan18-31_genomic.fna/target_genomes_gtdb.txt --output GCA_947445095.1_Jr-08jan18-31_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:19:25,870] [INFO] Task succeeded: fastANI
[2023-06-08 14:19:25,884] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:19:25,885] [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_013205645.1	s__Polaromonas sp013205645	85.9706	356	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941205.1	s__Polaromonas sp903941205	78.7831	281	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000709345.1	s__Polaromonas glacialis	78.1886	210	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780625.1	s__Polaromonas sp018780625	78.0819	215	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365105.1	s__Polaromonas sp010365105	78.0221	211	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817205.1	s__Polaromonas sp013817205	77.8684	186	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598235.1	s__Polaromonas jejuensis	77.8107	240	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844825.1	s__Polaromonas sp903844825	77.8022	206	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752205.1	s__Polaromonas sp015752205	77.7436	200	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	99.33	98.67	0.99	0.97	3	-
GCA_012927455.1	s__Polaromonas sp012927455	77.7278	220	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013865.1	s__Polaromonas sp000013865	77.7159	213	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688115.1	s__Polaromonas sp000688115	77.6207	204	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002381615.1	s__Polaromonas sp002381615	77.6043	199	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256925.1	s__Polaromonas sp002256925	77.4476	146	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	99.34	99.27	0.82	0.82	4	-
--------------------------------------------------------------------------------
[2023-06-08 14:19:25,887] [INFO] GTDB search result was written to GCA_947445095.1_Jr-08jan18-31_genomic.fna/result_gtdb.tsv
[2023-06-08 14:19:25,887] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:19:25,891] [INFO] DFAST_QC result json was written to GCA_947445095.1_Jr-08jan18-31_genomic.fna/dqc_result.json
[2023-06-08 14:19:25,891] [INFO] DFAST_QC completed!
[2023-06-08 14:19:25,891] [INFO] Total running time: 0h0m57s