[2023-06-29 07:57:13,340] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:57:13,342] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:57:13,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a9bcbfd-e9ac-45bf-93ca-7afd35a7f1ed/dqc_reference
[2023-06-29 07:57:16,303] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:57:16,304] [INFO] Task started: Prodigal
[2023-06-29 07:57:16,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg4adf5298-3b61-4d8b-b68e-eade9fd0a349/GCA_020430965.1_ASM2043096v1_genomic.fna.gz | prodigal -d GCA_020430965.1_ASM2043096v1_genomic.fna/cds.fna -a GCA_020430965.1_ASM2043096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:57:35,041] [INFO] Task succeeded: Prodigal
[2023-06-29 07:57:35,041] [INFO] Task started: HMMsearch
[2023-06-29 07:57:35,041] [INFO] Running command: hmmsearch --tblout GCA_020430965.1_ASM2043096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a9bcbfd-e9ac-45bf-93ca-7afd35a7f1ed/dqc_reference/reference_markers.hmm GCA_020430965.1_ASM2043096v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:57:35,320] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:57:35,321] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4adf5298-3b61-4d8b-b68e-eade9fd0a349/GCA_020430965.1_ASM2043096v1_genomic.fna.gz]
[2023-06-29 07:57:35,384] [INFO] Query marker FASTA was written to GCA_020430965.1_ASM2043096v1_genomic.fna/markers.fasta
[2023-06-29 07:57:35,385] [INFO] Task started: Blastn
[2023-06-29 07:57:35,385] [INFO] Running command: blastn -query GCA_020430965.1_ASM2043096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a9bcbfd-e9ac-45bf-93ca-7afd35a7f1ed/dqc_reference/reference_markers.fasta -out GCA_020430965.1_ASM2043096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:57:35,863] [INFO] Task succeeded: Blastn
[2023-06-29 07:57:35,866] [INFO] Selected 6 target genomes.
[2023-06-29 07:57:35,866] [INFO] Target genome list was writen to GCA_020430965.1_ASM2043096v1_genomic.fna/target_genomes.txt
[2023-06-29 07:57:35,868] [INFO] Task started: fastANI
[2023-06-29 07:57:35,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adf5298-3b61-4d8b-b68e-eade9fd0a349/GCA_020430965.1_ASM2043096v1_genomic.fna.gz --refList GCA_020430965.1_ASM2043096v1_genomic.fna/target_genomes.txt --output GCA_020430965.1_ASM2043096v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:57:43,639] [INFO] Task succeeded: fastANI
[2023-06-29 07:57:43,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a9bcbfd-e9ac-45bf-93ca-7afd35a7f1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:57:43,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a9bcbfd-e9ac-45bf-93ca-7afd35a7f1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:57:43,646] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:57:43,646] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 07:57:43,646] [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	75.1012	330	1679	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	74.9442	215	1679	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	74.8616	183	1679	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	74.6415	65	1679	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.5993	90	1679	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 07:57:43,648] [INFO] DFAST Taxonomy check result was written to GCA_020430965.1_ASM2043096v1_genomic.fna/tc_result.tsv
[2023-06-29 07:57:43,648] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:57:43,649] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:57:43,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a9bcbfd-e9ac-45bf-93ca-7afd35a7f1ed/dqc_reference/checkm_data
[2023-06-29 07:57:43,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:57:43,725] [INFO] Task started: CheckM
[2023-06-29 07:57:43,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020430965.1_ASM2043096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020430965.1_ASM2043096v1_genomic.fna/checkm_input GCA_020430965.1_ASM2043096v1_genomic.fna/checkm_result
[2023-06-29 07:58:37,673] [INFO] Task succeeded: CheckM
[2023-06-29 07:58:37,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 07:58:37,693] [INFO] ===== Completeness check finished =====
[2023-06-29 07:58:37,693] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:58:37,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020430965.1_ASM2043096v1_genomic.fna/markers.fasta)
[2023-06-29 07:58:37,693] [INFO] Task started: Blastn
[2023-06-29 07:58:37,694] [INFO] Running command: blastn -query GCA_020430965.1_ASM2043096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a9bcbfd-e9ac-45bf-93ca-7afd35a7f1ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_020430965.1_ASM2043096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:58:38,143] [INFO] Task succeeded: Blastn
[2023-06-29 07:58:38,147] [INFO] Selected 10 target genomes.
[2023-06-29 07:58:38,147] [INFO] Target genome list was writen to GCA_020430965.1_ASM2043096v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:58:38,150] [INFO] Task started: fastANI
[2023-06-29 07:58:38,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adf5298-3b61-4d8b-b68e-eade9fd0a349/GCA_020430965.1_ASM2043096v1_genomic.fna.gz --refList GCA_020430965.1_ASM2043096v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020430965.1_ASM2043096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:58:52,065] [INFO] Task succeeded: fastANI
[2023-06-29 07:58:52,073] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 07:58:52,074] [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_016875405.1	s__SYFR01 sp016875405	75.7637	177	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SYFR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005800325.1	s__SYFR01 sp005800325	75.5441	175	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SYFR01	95.0	99.65	99.65	0.86	0.86	2	-
GCA_016212965.1	s__JACRDA01 sp016212965	75.2794	387	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	75.1051	327	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	75.0301	389	1679	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	74.997	448	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_903906315.1	s__CAIVJW01 sp903906315	74.9837	324	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	74.9754	363	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213565.1	s__MED-G138 sp004213565	74.8385	269	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__MED-G138	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	74.7748	164	1679	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 07:58:52,076] [INFO] GTDB search result was written to GCA_020430965.1_ASM2043096v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:58:52,076] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:58:52,079] [INFO] DFAST_QC result json was written to GCA_020430965.1_ASM2043096v1_genomic.fna/dqc_result.json
[2023-06-29 07:58:52,079] [INFO] DFAST_QC completed!
[2023-06-29 07:58:52,079] [INFO] Total running time: 0h1m39s