[2023-06-13 08:07:58,636] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:58,639] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:58,639] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8f35a66-db2a-4b9f-b560-511916aeea4a/dqc_reference
[2023-06-13 08:07:59,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:59,951] [INFO] Task started: Prodigal
[2023-06-13 08:07:59,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b4b9bcd-e927-4dfa-ad85-fd0ed18eab7e/GCA_022449385.1_ASM2244938v1_genomic.fna.gz | prodigal -d GCA_022449385.1_ASM2244938v1_genomic.fna/cds.fna -a GCA_022449385.1_ASM2244938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:08:06,828] [INFO] Task succeeded: Prodigal
[2023-06-13 08:08:06,829] [INFO] Task started: HMMsearch
[2023-06-13 08:08:06,829] [INFO] Running command: hmmsearch --tblout GCA_022449385.1_ASM2244938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8f35a66-db2a-4b9f-b560-511916aeea4a/dqc_reference/reference_markers.hmm GCA_022449385.1_ASM2244938v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:08:07,070] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:08:07,071] [INFO] Found 6/6 markers.
[2023-06-13 08:08:07,095] [INFO] Query marker FASTA was written to GCA_022449385.1_ASM2244938v1_genomic.fna/markers.fasta
[2023-06-13 08:08:07,095] [INFO] Task started: Blastn
[2023-06-13 08:08:07,095] [INFO] Running command: blastn -query GCA_022449385.1_ASM2244938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f35a66-db2a-4b9f-b560-511916aeea4a/dqc_reference/reference_markers.fasta -out GCA_022449385.1_ASM2244938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:07,817] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:07,821] [INFO] Selected 26 target genomes.
[2023-06-13 08:08:07,821] [INFO] Target genome list was writen to GCA_022449385.1_ASM2244938v1_genomic.fna/target_genomes.txt
[2023-06-13 08:08:07,826] [INFO] Task started: fastANI
[2023-06-13 08:08:07,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b4b9bcd-e927-4dfa-ad85-fd0ed18eab7e/GCA_022449385.1_ASM2244938v1_genomic.fna.gz --refList GCA_022449385.1_ASM2244938v1_genomic.fna/target_genomes.txt --output GCA_022449385.1_ASM2244938v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:08:25,466] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:25,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8f35a66-db2a-4b9f-b560-511916aeea4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:08:25,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8f35a66-db2a-4b9f-b560-511916aeea4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:08:25,491] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:08:25,491] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:08:25,491] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.9559	166	722	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.9067	173	722	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.8412	132	722	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.1652	82	722	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.1119	131	722	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.987	89	722	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.9563	115	722	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	75.7301	75	722	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	75.5206	72	722	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	75.4873	98	722	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	75.402	70	722	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	75.4012	69	722	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	75.3247	113	722	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	75.3228	79	722	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	75.2623	55	722	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	75.2135	89	722	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	75.2044	69	722	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	75.1887	67	722	95	below_threshold
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	75.1877	65	722	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	75.1019	58	722	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	75.1019	58	722	95	below_threshold
Actinomycetospora endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	75.0963	102	722	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:08:25,493] [INFO] DFAST Taxonomy check result was written to GCA_022449385.1_ASM2244938v1_genomic.fna/tc_result.tsv
[2023-06-13 08:08:25,494] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:08:25,494] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:08:25,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8f35a66-db2a-4b9f-b560-511916aeea4a/dqc_reference/checkm_data
[2023-06-13 08:08:25,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:08:25,524] [INFO] Task started: CheckM
[2023-06-13 08:08:25,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022449385.1_ASM2244938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022449385.1_ASM2244938v1_genomic.fna/checkm_input GCA_022449385.1_ASM2244938v1_genomic.fna/checkm_result
[2023-06-13 08:08:51,155] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:51,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:51,178] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:51,178] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:51,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022449385.1_ASM2244938v1_genomic.fna/markers.fasta)
[2023-06-13 08:08:51,179] [INFO] Task started: Blastn
[2023-06-13 08:08:51,179] [INFO] Running command: blastn -query GCA_022449385.1_ASM2244938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f35a66-db2a-4b9f-b560-511916aeea4a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022449385.1_ASM2244938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:52,182] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:52,188] [INFO] Selected 13 target genomes.
[2023-06-13 08:08:52,188] [INFO] Target genome list was writen to GCA_022449385.1_ASM2244938v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:52,195] [INFO] Task started: fastANI
[2023-06-13 08:08:52,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b4b9bcd-e927-4dfa-ad85-fd0ed18eab7e/GCA_022449385.1_ASM2244938v1_genomic.fna.gz --refList GCA_022449385.1_ASM2244938v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022449385.1_ASM2244938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:58,319] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:58,331] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:08:58,331] [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_015658775.1	s__UBA3125 sp015658775	98.658	523	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	conclusive
GCA_016845305.1	s__UBA9410 sp016845305	79.6619	393	722	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_002346745.1	s__S20-B6 sp002346745	79.6075	355	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_018673475.1	s__UBA3125 sp018673475	79.3862	339	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.96	99.93	0.97	0.96	16	-
GCA_002687745.1	s__UBA3125 sp002687745	79.1069	313	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.98	96.61	0.89	0.87	5	-
GCA_012961035.1	s__UBA9410 sp012961035	79.0513	360	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014381745.1	s__UBA3125 sp014381745	79.0314	327	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.87	99.86	0.97	0.96	3	-
GCA_002329075.1	s__S20-B6 sp002329075	78.9909	346	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_014381945.1	s__S20-B6 sp014381945	78.9889	373	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501135.1	s__UBA3125 sp002501135	78.913	297	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.79	99.79	0.86	0.86	2	-
GCA_002365325.1	s__UBA3125 sp002365325	78.8102	281	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.82	97.98	0.79	0.76	7	-
GCA_014239855.1	s__UBA9410 sp014239855	78.8064	336	722	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:08:58,333] [INFO] GTDB search result was written to GCA_022449385.1_ASM2244938v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:58,334] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:58,338] [INFO] DFAST_QC result json was written to GCA_022449385.1_ASM2244938v1_genomic.fna/dqc_result.json
[2023-06-13 08:08:58,339] [INFO] DFAST_QC completed!
[2023-06-13 08:08:58,339] [INFO] Total running time: 0h0m60s