[2023-06-29 12:40:59,032] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:40:59,035] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:40:59,035] [INFO] DQC Reference Directory: /var/lib/cwl/stg81571d3a-059b-47c5-8f2b-9332e5c1cb00/dqc_reference
[2023-06-29 12:41:00,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:41:00,256] [INFO] Task started: Prodigal
[2023-06-29 12:41:00,257] [INFO] Running command: gunzip -c /var/lib/cwl/stge46ca922-f5e1-4128-84c6-e711a318425f/GCA_021848665.1_ASM2184866v1_genomic.fna.gz | prodigal -d GCA_021848665.1_ASM2184866v1_genomic.fna/cds.fna -a GCA_021848665.1_ASM2184866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:41:07,784] [INFO] Task succeeded: Prodigal
[2023-06-29 12:41:07,785] [INFO] Task started: HMMsearch
[2023-06-29 12:41:07,785] [INFO] Running command: hmmsearch --tblout GCA_021848665.1_ASM2184866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81571d3a-059b-47c5-8f2b-9332e5c1cb00/dqc_reference/reference_markers.hmm GCA_021848665.1_ASM2184866v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:41:08,008] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:41:08,010] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge46ca922-f5e1-4128-84c6-e711a318425f/GCA_021848665.1_ASM2184866v1_genomic.fna.gz]
[2023-06-29 12:41:08,042] [INFO] Query marker FASTA was written to GCA_021848665.1_ASM2184866v1_genomic.fna/markers.fasta
[2023-06-29 12:41:08,043] [INFO] Task started: Blastn
[2023-06-29 12:41:08,043] [INFO] Running command: blastn -query GCA_021848665.1_ASM2184866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81571d3a-059b-47c5-8f2b-9332e5c1cb00/dqc_reference/reference_markers.fasta -out GCA_021848665.1_ASM2184866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:08,558] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:08,563] [INFO] Selected 6 target genomes.
[2023-06-29 12:41:08,564] [INFO] Target genome list was writen to GCA_021848665.1_ASM2184866v1_genomic.fna/target_genomes.txt
[2023-06-29 12:41:08,566] [INFO] Task started: fastANI
[2023-06-29 12:41:08,566] [INFO] Running command: fastANI --query /var/lib/cwl/stge46ca922-f5e1-4128-84c6-e711a318425f/GCA_021848665.1_ASM2184866v1_genomic.fna.gz --refList GCA_021848665.1_ASM2184866v1_genomic.fna/target_genomes.txt --output GCA_021848665.1_ASM2184866v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:41:12,163] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:12,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81571d3a-059b-47c5-8f2b-9332e5c1cb00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:41:12,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81571d3a-059b-47c5-8f2b-9332e5c1cb00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:41:12,177] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:41:12,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:41:12,178] [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
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	78.9123	165	666	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.5152	160	666	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.5138	158	666	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	77.6861	151	666	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	77.4575	118	666	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	77.0438	120	666	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:41:12,180] [INFO] DFAST Taxonomy check result was written to GCA_021848665.1_ASM2184866v1_genomic.fna/tc_result.tsv
[2023-06-29 12:41:12,181] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:41:12,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:41:12,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81571d3a-059b-47c5-8f2b-9332e5c1cb00/dqc_reference/checkm_data
[2023-06-29 12:41:12,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:41:12,223] [INFO] Task started: CheckM
[2023-06-29 12:41:12,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021848665.1_ASM2184866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021848665.1_ASM2184866v1_genomic.fna/checkm_input GCA_021848665.1_ASM2184866v1_genomic.fna/checkm_result
[2023-06-29 12:41:39,404] [INFO] Task succeeded: CheckM
[2023-06-29 12:41:39,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:41:39,426] [INFO] ===== Completeness check finished =====
[2023-06-29 12:41:39,426] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:41:39,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021848665.1_ASM2184866v1_genomic.fna/markers.fasta)
[2023-06-29 12:41:39,427] [INFO] Task started: Blastn
[2023-06-29 12:41:39,427] [INFO] Running command: blastn -query GCA_021848665.1_ASM2184866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81571d3a-059b-47c5-8f2b-9332e5c1cb00/dqc_reference/reference_markers_gtdb.fasta -out GCA_021848665.1_ASM2184866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:39,941] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:39,945] [INFO] Selected 7 target genomes.
[2023-06-29 12:41:39,945] [INFO] Target genome list was writen to GCA_021848665.1_ASM2184866v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:41:39,971] [INFO] Task started: fastANI
[2023-06-29 12:41:39,971] [INFO] Running command: fastANI --query /var/lib/cwl/stge46ca922-f5e1-4128-84c6-e711a318425f/GCA_021848665.1_ASM2184866v1_genomic.fna.gz --refList GCA_021848665.1_ASM2184866v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021848665.1_ASM2184866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:41:44,120] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:44,128] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:41:44,128] [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
GCF_016858125.1	s__Azospira_A restricta	81.6499	276	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183655.1	s__Azospira_A sp016183655	81.5693	251	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710885.1	s__Azospira_A sp016710885	80.7202	154	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	98.08	98.08	0.87	0.87	2	-
GCF_003634965.1	s__Azonexus fungiphilus	78.9128	165	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.36	98.36	0.85	0.85	2	-
GCF_014197755.1	s__Rhodocyclus tenuis	78.5384	159	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.79	97.58	0.96	0.93	3	-
GCF_004217225.1	s__Azospira oryzae	77.6719	151	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira	95.0	98.24	98.03	0.94	0.90	6	-
GCA_002304785.1	s__Propionivibrio sp002304785	77.5366	98	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:41:44,130] [INFO] GTDB search result was written to GCA_021848665.1_ASM2184866v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:41:44,131] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:41:44,134] [INFO] DFAST_QC result json was written to GCA_021848665.1_ASM2184866v1_genomic.fna/dqc_result.json
[2023-06-29 12:41:44,134] [INFO] DFAST_QC completed!
[2023-06-29 12:41:44,134] [INFO] Total running time: 0h0m45s