[2024-01-24 12:36:58,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc6ba175-3335-4504-a119-cd43c7865014/dqc_reference
[2024-01-24 12:36:59,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,854] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e510545-64d6-4904-ad93-dfd087ed2b37/GCF_018436245.1_ASM1843624v1_genomic.fna.gz | prodigal -d GCF_018436245.1_ASM1843624v1_genomic.fna/cds.fna -a GCF_018436245.1_ASM1843624v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:11,457] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:11,458] [INFO] Task started: HMMsearch
[2024-01-24 12:37:11,458] [INFO] Running command: hmmsearch --tblout GCF_018436245.1_ASM1843624v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc6ba175-3335-4504-a119-cd43c7865014/dqc_reference/reference_markers.hmm GCF_018436245.1_ASM1843624v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:11,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:11,805] [INFO] Found 6/6 markers.
[2024-01-24 12:37:11,844] [INFO] Query marker FASTA was written to GCF_018436245.1_ASM1843624v1_genomic.fna/markers.fasta
[2024-01-24 12:37:11,847] [INFO] Task started: Blastn
[2024-01-24 12:37:11,848] [INFO] Running command: blastn -query GCF_018436245.1_ASM1843624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc6ba175-3335-4504-a119-cd43c7865014/dqc_reference/reference_markers.fasta -out GCF_018436245.1_ASM1843624v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:12,592] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:12,630] [INFO] Selected 8 target genomes.
[2024-01-24 12:37:12,630] [INFO] Target genome list was writen to GCF_018436245.1_ASM1843624v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:12,648] [INFO] Task started: fastANI
[2024-01-24 12:37:12,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e510545-64d6-4904-ad93-dfd087ed2b37/GCF_018436245.1_ASM1843624v1_genomic.fna.gz --refList GCF_018436245.1_ASM1843624v1_genomic.fna/target_genomes.txt --output GCF_018436245.1_ASM1843624v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:20,604] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:20,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc6ba175-3335-4504-a119-cd43c7865014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:20,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc6ba175-3335-4504-a119-cd43c7865014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:20,614] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:37:20,614] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:37:20,614] [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
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	100.0	1329	1332	95	inconclusive
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	100.0	1329	1332	95	inconclusive
Pseudochrobactrum saccharolyticum	strain=DSM 25620	GCA_014203195.1	354352	354352	type	True	96.2304	1172	1332	95	inconclusive
Pseudochrobactrum saccharolyticum	strain=CCUG 33852	GCA_008801715.1	354352	354352	type	True	96.2238	1172	1332	95	inconclusive
Pseudochrobactrum asaccharolyticum	strain=DSM 25619	GCA_003314995.1	354351	354351	type	True	86.9277	1035	1332	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.8944	141	1332	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	76.6367	100	1332	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	76.2544	84	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:20,616] [INFO] DFAST Taxonomy check result was written to GCF_018436245.1_ASM1843624v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:20,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:20,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:20,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc6ba175-3335-4504-a119-cd43c7865014/dqc_reference/checkm_data
[2024-01-24 12:37:20,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:20,663] [INFO] Task started: CheckM
[2024-01-24 12:37:20,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018436245.1_ASM1843624v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018436245.1_ASM1843624v1_genomic.fna/checkm_input GCF_018436245.1_ASM1843624v1_genomic.fna/checkm_result
[2024-01-24 12:38:01,367] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:01,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:01,397] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:01,397] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:01,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018436245.1_ASM1843624v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:01,397] [INFO] Task started: Blastn
[2024-01-24 12:38:01,397] [INFO] Running command: blastn -query GCF_018436245.1_ASM1843624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc6ba175-3335-4504-a119-cd43c7865014/dqc_reference/reference_markers_gtdb.fasta -out GCF_018436245.1_ASM1843624v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:02,490] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:02,494] [INFO] Selected 16 target genomes.
[2024-01-24 12:38:02,495] [INFO] Target genome list was writen to GCF_018436245.1_ASM1843624v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:02,517] [INFO] Task started: fastANI
[2024-01-24 12:38:02,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e510545-64d6-4904-ad93-dfd087ed2b37/GCF_018436245.1_ASM1843624v1_genomic.fna.gz --refList GCF_018436245.1_ASM1843624v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018436245.1_ASM1843624v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:16,716] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:16,729] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:16,729] [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_008801715.1	s__Pseudochrobactrum saccharolyticum	96.2238	1172	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	96.83	96.24	0.94	0.92	10	conclusive
GCA_900470285.1	s__Pseudochrobactrum sp900470285	93.1736	1107	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	97.83	97.83	0.89	0.89	2	-
GCF_003314995.1	s__Pseudochrobactrum asaccharolyticum	86.9277	1035	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	95.18	95.14	0.85	0.85	3	-
GCF_014205685.1	s__Paenochrobactrum gallinarii	79.0841	341	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paenochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278035.1	s__Ochrobactrum_A quorumnocens	78.3377	267	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.19	96.78	0.85	0.82	5	-
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	78.2248	298	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.50	96.15	0.90	0.81	34	-
GCF_006476605.1	s__Ochrobactrum_A gallinifaecis	78.2186	250	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252475.1	s__Ochrobactrum_A rhizosphaerae	77.8568	258	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975205.1	s__Ochrobactrum sp002975205	77.8346	290	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007125.1	s__Brucella melitensis	77.7792	252	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Brucella	95.0	99.71	97.51	0.99	0.88	877	-
GCF_006376685.1	s__Ochrobactrum_B teleogrylli	77.6957	313	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.13	98.09	0.91	0.90	5	-
GCA_900465685.1	s__Ochrobactrum_B sp900465685	77.4877	330	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	99.22	99.21	0.91	0.91	3	-
GCF_003149535.1	s__Falsochrobactrum shanghaiense	77.4192	269	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980495.1	s__Paramesorhizobium phragmitis	76.8083	214	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197535.1	s__Rhizobium aethiopicum_A	76.3014	89	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:16,731] [INFO] GTDB search result was written to GCF_018436245.1_ASM1843624v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:16,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:16,739] [INFO] DFAST_QC result json was written to GCF_018436245.1_ASM1843624v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:16,740] [INFO] DFAST_QC completed!
[2024-01-24 12:38:16,740] [INFO] Total running time: 0h1m18s