[2023-06-28 10:27:47,613] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:27:47,615] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:27:47,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1e025db-3df9-4551-ae34-ff373100469d/dqc_reference
[2023-06-28 10:27:48,804] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:27:48,804] [INFO] Task started: Prodigal
[2023-06-28 10:27:48,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgcea963f7-88e1-42a9-92de-7849f21612cc/GCA_005805165.1_ASM580516v1_genomic.fna.gz | prodigal -d GCA_005805165.1_ASM580516v1_genomic.fna/cds.fna -a GCA_005805165.1_ASM580516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:27:57,224] [INFO] Task succeeded: Prodigal
[2023-06-28 10:27:57,224] [INFO] Task started: HMMsearch
[2023-06-28 10:27:57,225] [INFO] Running command: hmmsearch --tblout GCA_005805165.1_ASM580516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1e025db-3df9-4551-ae34-ff373100469d/dqc_reference/reference_markers.hmm GCA_005805165.1_ASM580516v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:27:57,484] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:27:57,486] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcea963f7-88e1-42a9-92de-7849f21612cc/GCA_005805165.1_ASM580516v1_genomic.fna.gz]
[2023-06-28 10:27:57,529] [INFO] Query marker FASTA was written to GCA_005805165.1_ASM580516v1_genomic.fna/markers.fasta
[2023-06-28 10:27:57,530] [INFO] Task started: Blastn
[2023-06-28 10:27:57,530] [INFO] Running command: blastn -query GCA_005805165.1_ASM580516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e025db-3df9-4551-ae34-ff373100469d/dqc_reference/reference_markers.fasta -out GCA_005805165.1_ASM580516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:27:58,112] [INFO] Task succeeded: Blastn
[2023-06-28 10:27:58,117] [INFO] Selected 20 target genomes.
[2023-06-28 10:27:58,118] [INFO] Target genome list was writen to GCA_005805165.1_ASM580516v1_genomic.fna/target_genomes.txt
[2023-06-28 10:27:58,119] [INFO] Task started: fastANI
[2023-06-28 10:27:58,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgcea963f7-88e1-42a9-92de-7849f21612cc/GCA_005805165.1_ASM580516v1_genomic.fna.gz --refList GCA_005805165.1_ASM580516v1_genomic.fna/target_genomes.txt --output GCA_005805165.1_ASM580516v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:28:15,699] [INFO] Task succeeded: fastANI
[2023-06-28 10:28:15,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1e025db-3df9-4551-ae34-ff373100469d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:28:15,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1e025db-3df9-4551-ae34-ff373100469d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:28:15,712] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:28:15,713] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:28:15,713] [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
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.5806	397	996	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.5492	373	996	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.545	382	996	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.3418	191	996	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	74.6749	55	996	95	below_threshold
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	74.604	51	996	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.5986	145	996	95	below_threshold
Caballeronia telluris		GCA_001544495.2	326475	326475	type	True	74.5659	100	996	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	74.5559	90	996	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:28:15,716] [INFO] DFAST Taxonomy check result was written to GCA_005805165.1_ASM580516v1_genomic.fna/tc_result.tsv
[2023-06-28 10:28:15,716] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:28:15,716] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:28:15,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1e025db-3df9-4551-ae34-ff373100469d/dqc_reference/checkm_data
[2023-06-28 10:28:15,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:28:15,757] [INFO] Task started: CheckM
[2023-06-28 10:28:15,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005805165.1_ASM580516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005805165.1_ASM580516v1_genomic.fna/checkm_input GCA_005805165.1_ASM580516v1_genomic.fna/checkm_result
[2023-06-28 10:28:44,408] [INFO] Task succeeded: CheckM
[2023-06-28 10:28:44,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:28:44,432] [INFO] ===== Completeness check finished =====
[2023-06-28 10:28:44,432] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:28:44,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005805165.1_ASM580516v1_genomic.fna/markers.fasta)
[2023-06-28 10:28:44,433] [INFO] Task started: Blastn
[2023-06-28 10:28:44,433] [INFO] Running command: blastn -query GCA_005805165.1_ASM580516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e025db-3df9-4551-ae34-ff373100469d/dqc_reference/reference_markers_gtdb.fasta -out GCA_005805165.1_ASM580516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:28:45,242] [INFO] Task succeeded: Blastn
[2023-06-28 10:28:45,248] [INFO] Selected 17 target genomes.
[2023-06-28 10:28:45,248] [INFO] Target genome list was writen to GCA_005805165.1_ASM580516v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:28:45,252] [INFO] Task started: fastANI
[2023-06-28 10:28:45,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgcea963f7-88e1-42a9-92de-7849f21612cc/GCA_005805165.1_ASM580516v1_genomic.fna.gz --refList GCA_005805165.1_ASM580516v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005805165.1_ASM580516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:29:05,764] [INFO] Task succeeded: fastANI
[2023-06-28 10:29:05,783] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:29:05,783] [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_005800325.1	s__SYFR01 sp005800325	99.6727	856	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SYFR01	95.0	99.65	99.65	0.86	0.86	2	conclusive
GCA_009692485.1	s__SYFR01 sp009692485	78.5679	494	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SYFR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875405.1	s__SYFR01 sp016875405	76.8577	374	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SYFR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212965.1	s__JACRDA01 sp016212965	75.9999	449	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906315.1	s__CAIVJW01 sp903906315	75.6557	398	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	75.5434	392	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	75.522	411	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	75.4256	460	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_016719945.1	s__CAITIQ01 sp016719945	75.4007	289	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	99.43	99.43	0.95	0.95	2	-
GCA_903893335.1	s__CAITLX01 sp903893335	75.3093	294	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794345.1	s__CAITIQ01 sp016794345	75.2952	281	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303575.1	s__JAFLCL01 sp017303575	74.9941	288	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001263205.1	s__Labilithrix luteola	74.9734	201	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298325.1	s__JAAFHJ01 sp013298325	74.7678	57	996	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969685.1	s__UBA3006 sp018969685	74.6635	51	996	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:29:05,785] [INFO] GTDB search result was written to GCA_005805165.1_ASM580516v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:29:05,786] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:29:05,789] [INFO] DFAST_QC result json was written to GCA_005805165.1_ASM580516v1_genomic.fna/dqc_result.json
[2023-06-28 10:29:05,789] [INFO] DFAST_QC completed!
[2023-06-28 10:29:05,790] [INFO] Total running time: 0h1m18s