[2023-06-27 22:27:35,290] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:27:35,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:27:35,295] [INFO] DQC Reference Directory: /var/lib/cwl/stgd536eaf7-da15-456c-b21c-46e13e99d7b1/dqc_reference
[2023-06-27 22:27:38,485] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:27:38,486] [INFO] Task started: Prodigal
[2023-06-27 22:27:38,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg1531d82b-85fb-45da-9446-83d11cb3e3bf/GCA_026706815.1_ASM2670681v1_genomic.fna.gz | prodigal -d GCA_026706815.1_ASM2670681v1_genomic.fna/cds.fna -a GCA_026706815.1_ASM2670681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:27:47,687] [INFO] Task succeeded: Prodigal
[2023-06-27 22:27:47,687] [INFO] Task started: HMMsearch
[2023-06-27 22:27:47,688] [INFO] Running command: hmmsearch --tblout GCA_026706815.1_ASM2670681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd536eaf7-da15-456c-b21c-46e13e99d7b1/dqc_reference/reference_markers.hmm GCA_026706815.1_ASM2670681v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:27:47,931] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:27:47,933] [INFO] Found 6/6 markers.
[2023-06-27 22:27:47,979] [INFO] Query marker FASTA was written to GCA_026706815.1_ASM2670681v1_genomic.fna/markers.fasta
[2023-06-27 22:27:47,980] [INFO] Task started: Blastn
[2023-06-27 22:27:47,980] [INFO] Running command: blastn -query GCA_026706815.1_ASM2670681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd536eaf7-da15-456c-b21c-46e13e99d7b1/dqc_reference/reference_markers.fasta -out GCA_026706815.1_ASM2670681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:27:48,682] [INFO] Task succeeded: Blastn
[2023-06-27 22:27:48,687] [INFO] Selected 29 target genomes.
[2023-06-27 22:27:48,687] [INFO] Target genome list was writen to GCA_026706815.1_ASM2670681v1_genomic.fna/target_genomes.txt
[2023-06-27 22:27:48,727] [INFO] Task started: fastANI
[2023-06-27 22:27:48,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg1531d82b-85fb-45da-9446-83d11cb3e3bf/GCA_026706815.1_ASM2670681v1_genomic.fna.gz --refList GCA_026706815.1_ASM2670681v1_genomic.fna/target_genomes.txt --output GCA_026706815.1_ASM2670681v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:28:08,870] [INFO] Task succeeded: fastANI
[2023-06-27 22:28:08,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd536eaf7-da15-456c-b21c-46e13e99d7b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:28:08,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd536eaf7-da15-456c-b21c-46e13e99d7b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:28:08,882] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:28:08,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 22:28:08,882] [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
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.3576	57	980	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.2655	71	980	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1124	99	980	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.0857	91	980	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.9313	75	980	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	75.254	57	980	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	74.952	54	980	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	74.948	55	980	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 22:28:08,884] [INFO] DFAST Taxonomy check result was written to GCA_026706815.1_ASM2670681v1_genomic.fna/tc_result.tsv
[2023-06-27 22:28:08,885] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:28:08,885] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:28:08,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd536eaf7-da15-456c-b21c-46e13e99d7b1/dqc_reference/checkm_data
[2023-06-27 22:28:08,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:28:08,919] [INFO] Task started: CheckM
[2023-06-27 22:28:08,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026706815.1_ASM2670681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026706815.1_ASM2670681v1_genomic.fna/checkm_input GCA_026706815.1_ASM2670681v1_genomic.fna/checkm_result
[2023-06-27 22:28:40,472] [INFO] Task succeeded: CheckM
[2023-06-27 22:28:40,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:28:40,494] [INFO] ===== Completeness check finished =====
[2023-06-27 22:28:40,494] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:28:40,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026706815.1_ASM2670681v1_genomic.fna/markers.fasta)
[2023-06-27 22:28:40,495] [INFO] Task started: Blastn
[2023-06-27 22:28:40,496] [INFO] Running command: blastn -query GCA_026706815.1_ASM2670681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd536eaf7-da15-456c-b21c-46e13e99d7b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_026706815.1_ASM2670681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:28:41,838] [INFO] Task succeeded: Blastn
[2023-06-27 22:28:41,843] [INFO] Selected 22 target genomes.
[2023-06-27 22:28:41,843] [INFO] Target genome list was writen to GCA_026706815.1_ASM2670681v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:28:41,890] [INFO] Task started: fastANI
[2023-06-27 22:28:41,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg1531d82b-85fb-45da-9446-83d11cb3e3bf/GCA_026706815.1_ASM2670681v1_genomic.fna.gz --refList GCA_026706815.1_ASM2670681v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026706815.1_ASM2670681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:28:54,398] [INFO] Task succeeded: fastANI
[2023-06-27 22:28:54,413] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 22:28:54,413] [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_009845995.1	s__VXYK01 sp009845995	87.9047	769	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VXYK01	95.0	99.45	99.19	0.95	0.93	8	-
GCA_002694825.1	s__UBA11606 sp002694825	77.1117	150	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_009844405.1	s__VYCW01 sp009844405	77.0876	164	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.44	99.17	0.93	0.90	7	-
GCA_009843915.1	s__VYCW01 sp009843915	77.0574	140	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	97.45	96.57	0.82	0.78	5	-
GCA_016845305.1	s__UBA9410 sp016845305	77.0189	103	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009842325.1	s__VYCW01 sp009842325	76.9824	175	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.89	99.81	0.98	0.97	3	-
GCA_002699625.1	s__UBA11606 sp002699625	76.9723	117	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729125.1	s__UBA11606 sp002729125	76.7474	117	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_009837445.1	s__VYCW01 sp009837445	76.7258	174	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.43	98.40	0.97	0.95	9	-
GCA_003231645.1	s__SZUA-87 sp003231645	76.7066	105	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__SZUA-87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845585.1	s__UBA11606 sp016845585	76.6363	173	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.6093	101	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843735.1	s__VYCW01 sp009843735	76.6013	161	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.31	99.30	0.93	0.93	3	-
GCA_009937405.1	s__UBA11606 sp009937405	76.4421	77	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	76.3576	57	980	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:28:54,415] [INFO] GTDB search result was written to GCA_026706815.1_ASM2670681v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:28:54,416] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:28:54,419] [INFO] DFAST_QC result json was written to GCA_026706815.1_ASM2670681v1_genomic.fna/dqc_result.json
[2023-06-27 22:28:54,420] [INFO] DFAST_QC completed!
[2023-06-27 22:28:54,420] [INFO] Total running time: 0h1m19s