[2023-06-13 08:07:27,228] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:27,232] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:27,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5e2b620-5cb7-467f-91b2-6063edd07de3/dqc_reference
[2023-06-13 08:07:28,426] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:28,426] [INFO] Task started: Prodigal
[2023-06-13 08:07:28,427] [INFO] Running command: gunzip -c /var/lib/cwl/stgd287d649-3ed5-44fd-a307-fb7d7767c365/GCA_022072125.1_ASM2207212v1_genomic.fna.gz | prodigal -d GCA_022072125.1_ASM2207212v1_genomic.fna/cds.fna -a GCA_022072125.1_ASM2207212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:41,445] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:41,445] [INFO] Task started: HMMsearch
[2023-06-13 08:07:41,446] [INFO] Running command: hmmsearch --tblout GCA_022072125.1_ASM2207212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5e2b620-5cb7-467f-91b2-6063edd07de3/dqc_reference/reference_markers.hmm GCA_022072125.1_ASM2207212v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:41,675] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:41,676] [INFO] Found 6/6 markers.
[2023-06-13 08:07:41,710] [INFO] Query marker FASTA was written to GCA_022072125.1_ASM2207212v1_genomic.fna/markers.fasta
[2023-06-13 08:07:41,711] [INFO] Task started: Blastn
[2023-06-13 08:07:41,711] [INFO] Running command: blastn -query GCA_022072125.1_ASM2207212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5e2b620-5cb7-467f-91b2-6063edd07de3/dqc_reference/reference_markers.fasta -out GCA_022072125.1_ASM2207212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:42,384] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:42,392] [INFO] Selected 25 target genomes.
[2023-06-13 08:07:42,392] [INFO] Target genome list was writen to GCA_022072125.1_ASM2207212v1_genomic.fna/target_genomes.txt
[2023-06-13 08:07:42,398] [INFO] Task started: fastANI
[2023-06-13 08:07:42,399] [INFO] Running command: fastANI --query /var/lib/cwl/stgd287d649-3ed5-44fd-a307-fb7d7767c365/GCA_022072125.1_ASM2207212v1_genomic.fna.gz --refList GCA_022072125.1_ASM2207212v1_genomic.fna/target_genomes.txt --output GCA_022072125.1_ASM2207212v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:08:02,433] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:02,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5e2b620-5cb7-467f-91b2-6063edd07de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:08:02,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5e2b620-5cb7-467f-91b2-6063edd07de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:08:02,441] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:08:02,441] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:08:02,441] [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
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.652	63	1288	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.4957	75	1288	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	75.3852	55	1288	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.3516	85	1288	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	75.2913	62	1288	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	75.1951	104	1288	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	75.1782	60	1288	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:08:02,443] [INFO] DFAST Taxonomy check result was written to GCA_022072125.1_ASM2207212v1_genomic.fna/tc_result.tsv
[2023-06-13 08:08:02,444] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:08:02,444] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:08:02,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5e2b620-5cb7-467f-91b2-6063edd07de3/dqc_reference/checkm_data
[2023-06-13 08:08:02,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:08:02,487] [INFO] Task started: CheckM
[2023-06-13 08:08:02,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022072125.1_ASM2207212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022072125.1_ASM2207212v1_genomic.fna/checkm_input GCA_022072125.1_ASM2207212v1_genomic.fna/checkm_result
[2023-06-13 08:08:47,614] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:47,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:47,631] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:47,631] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:47,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022072125.1_ASM2207212v1_genomic.fna/markers.fasta)
[2023-06-13 08:08:47,632] [INFO] Task started: Blastn
[2023-06-13 08:08:47,632] [INFO] Running command: blastn -query GCA_022072125.1_ASM2207212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5e2b620-5cb7-467f-91b2-6063edd07de3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022072125.1_ASM2207212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:48,640] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:48,644] [INFO] Selected 23 target genomes.
[2023-06-13 08:08:48,644] [INFO] Target genome list was writen to GCA_022072125.1_ASM2207212v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:48,656] [INFO] Task started: fastANI
[2023-06-13 08:08:48,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgd287d649-3ed5-44fd-a307-fb7d7767c365/GCA_022072125.1_ASM2207212v1_genomic.fna.gz --refList GCA_022072125.1_ASM2207212v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022072125.1_ASM2207212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:09:05,057] [INFO] Task succeeded: fastANI
[2023-06-13 08:09:05,068] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 08:09:05,068] [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_000165485.1	s__Stigmatella aurantiaca_A	75.6766	67	1288	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_012798435.1	s__JAAZNF01 sp012798435	75.5692	60	1288	d__Bacteria;p__Myxococcota;c__B64-G9;o__B64-G9;f__B64-G9;g__JAAZNF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718565.1	s__JADKCZ01 sp016718565	75.554	110	1288	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JADKCZ01	95.0	99.81	99.81	0.97	0.97	2	-
GCF_900109545.1	s__Stigmatella aurantiaca	75.51	74	1288	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCA_005888115.1	s__40CM-4-68-19 sp005888115	75.4641	59	1288	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__40CM-4-68-19;g__40CM-4-68-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009759665.1	s__Bradyrhizobium cajani	75.3852	55	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.56	95.54	0.80	0.80	3	-
GCA_900696455.1	s__UBA2376 sp900696455	75.2551	125	1288	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCF_018069875.1	s__Ideonella sp018069875	75.1942	70	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCA_016707895.1	s__UBA2376 sp016707895	75.115	119	1288	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_011368045.1	s__JAAZNF01 sp011368045	75.1107	56	1288	d__Bacteria;p__Myxococcota;c__B64-G9;o__B64-G9;f__B64-G9;g__JAAZNF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	75.0515	129	1288	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906305.1	s__Alcanivorax marinus_B	74.9888	50	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:09:05,070] [INFO] GTDB search result was written to GCA_022072125.1_ASM2207212v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:09:05,070] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:09:05,073] [INFO] DFAST_QC result json was written to GCA_022072125.1_ASM2207212v1_genomic.fna/dqc_result.json
[2023-06-13 08:09:05,073] [INFO] DFAST_QC completed!
[2023-06-13 08:09:05,074] [INFO] Total running time: 0h1m38s