[2023-06-28 10:46:09,931] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:46:09,937] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:46:09,937] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7cd700d-53d4-4414-8138-463717d66af1/dqc_reference
[2023-06-28 10:46:11,318] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:46:11,319] [INFO] Task started: Prodigal
[2023-06-28 10:46:11,319] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cf2c9b3-7033-4bc1-8fe7-e631655e1556/GCA_019310905.1_ASM1931090v1_genomic.fna.gz | prodigal -d GCA_019310905.1_ASM1931090v1_genomic.fna/cds.fna -a GCA_019310905.1_ASM1931090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:46:20,069] [INFO] Task succeeded: Prodigal
[2023-06-28 10:46:20,070] [INFO] Task started: HMMsearch
[2023-06-28 10:46:20,070] [INFO] Running command: hmmsearch --tblout GCA_019310905.1_ASM1931090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7cd700d-53d4-4414-8138-463717d66af1/dqc_reference/reference_markers.hmm GCA_019310905.1_ASM1931090v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:46:20,373] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:46:20,375] [INFO] Found 6/6 markers.
[2023-06-28 10:46:20,410] [INFO] Query marker FASTA was written to GCA_019310905.1_ASM1931090v1_genomic.fna/markers.fasta
[2023-06-28 10:46:20,410] [INFO] Task started: Blastn
[2023-06-28 10:46:20,411] [INFO] Running command: blastn -query GCA_019310905.1_ASM1931090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7cd700d-53d4-4414-8138-463717d66af1/dqc_reference/reference_markers.fasta -out GCA_019310905.1_ASM1931090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:46:21,220] [INFO] Task succeeded: Blastn
[2023-06-28 10:46:21,223] [INFO] Selected 28 target genomes.
[2023-06-28 10:46:21,224] [INFO] Target genome list was writen to GCA_019310905.1_ASM1931090v1_genomic.fna/target_genomes.txt
[2023-06-28 10:46:21,234] [INFO] Task started: fastANI
[2023-06-28 10:46:21,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf2c9b3-7033-4bc1-8fe7-e631655e1556/GCA_019310905.1_ASM1931090v1_genomic.fna.gz --refList GCA_019310905.1_ASM1931090v1_genomic.fna/target_genomes.txt --output GCA_019310905.1_ASM1931090v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:46:52,166] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:52,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7cd700d-53d4-4414-8138-463717d66af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:46:52,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7cd700d-53d4-4414-8138-463717d66af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:46:52,177] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:46:52,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:46:52,178] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.9283	116	817	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.2491	69	817	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.2195	66	817	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.1718	71	817	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.1012	84	817	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:46:52,180] [INFO] DFAST Taxonomy check result was written to GCA_019310905.1_ASM1931090v1_genomic.fna/tc_result.tsv
[2023-06-28 10:46:52,181] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:46:52,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:46:52,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7cd700d-53d4-4414-8138-463717d66af1/dqc_reference/checkm_data
[2023-06-28 10:46:52,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:46:52,229] [INFO] Task started: CheckM
[2023-06-28 10:46:52,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310905.1_ASM1931090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310905.1_ASM1931090v1_genomic.fna/checkm_input GCA_019310905.1_ASM1931090v1_genomic.fna/checkm_result
[2023-06-28 10:47:22,404] [INFO] Task succeeded: CheckM
[2023-06-28 10:47:22,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.06%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 10:47:22,431] [INFO] ===== Completeness check finished =====
[2023-06-28 10:47:22,432] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:47:22,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310905.1_ASM1931090v1_genomic.fna/markers.fasta)
[2023-06-28 10:47:22,433] [INFO] Task started: Blastn
[2023-06-28 10:47:22,433] [INFO] Running command: blastn -query GCA_019310905.1_ASM1931090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7cd700d-53d4-4414-8138-463717d66af1/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310905.1_ASM1931090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:23,714] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:23,719] [INFO] Selected 17 target genomes.
[2023-06-28 10:47:23,720] [INFO] Target genome list was writen to GCA_019310905.1_ASM1931090v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:47:23,730] [INFO] Task started: fastANI
[2023-06-28 10:47:23,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf2c9b3-7033-4bc1-8fe7-e631655e1556/GCA_019310905.1_ASM1931090v1_genomic.fna.gz --refList GCA_019310905.1_ASM1931090v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310905.1_ASM1931090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:47:36,578] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:36,591] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:47:36,591] [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_003647035.1	s__SG8-38 sp003647035	81.5596	473	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	96.70	96.70	0.74	0.74	2	-
GCA_004283055.1	s__SG8-38 sp004283055	78.6046	416	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	99.78	99.72	0.93	0.90	8	-
GCA_013002645.1	s__SG8-38 sp013002645	78.4299	338	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001303415.1	s__SG8-38 sp001303415	77.6457	284	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644045.1	s__UBA1660 sp017644045	76.4416	110	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	75.9092	136	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_003647065.1	s__B10-G4 sp003647065	75.741	55	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__B10-G4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	75.5103	107	817	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:47:36,593] [INFO] GTDB search result was written to GCA_019310905.1_ASM1931090v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:47:36,594] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:47:36,597] [INFO] DFAST_QC result json was written to GCA_019310905.1_ASM1931090v1_genomic.fna/dqc_result.json
[2023-06-28 10:47:36,597] [INFO] DFAST_QC completed!
[2023-06-28 10:47:36,597] [INFO] Total running time: 0h1m27s