[2023-07-01 01:53:44,397] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:53:44,399] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:53:44,399] [INFO] DQC Reference Directory: /var/lib/cwl/stge20729ef-e6ae-4945-b868-b94238743262/dqc_reference
[2023-07-01 01:53:45,622] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:53:45,623] [INFO] Task started: Prodigal
[2023-07-01 01:53:45,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b6c14ff-6e01-45cf-84b9-79f4683e115a/GCA_025930595.1_ASM2593059v1_genomic.fna.gz | prodigal -d GCA_025930595.1_ASM2593059v1_genomic.fna/cds.fna -a GCA_025930595.1_ASM2593059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:53:55,543] [INFO] Task succeeded: Prodigal
[2023-07-01 01:53:55,543] [INFO] Task started: HMMsearch
[2023-07-01 01:53:55,543] [INFO] Running command: hmmsearch --tblout GCA_025930595.1_ASM2593059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge20729ef-e6ae-4945-b868-b94238743262/dqc_reference/reference_markers.hmm GCA_025930595.1_ASM2593059v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:53:55,783] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:53:55,784] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2b6c14ff-6e01-45cf-84b9-79f4683e115a/GCA_025930595.1_ASM2593059v1_genomic.fna.gz]
[2023-07-01 01:53:55,845] [INFO] Query marker FASTA was written to GCA_025930595.1_ASM2593059v1_genomic.fna/markers.fasta
[2023-07-01 01:53:55,846] [INFO] Task started: Blastn
[2023-07-01 01:53:55,846] [INFO] Running command: blastn -query GCA_025930595.1_ASM2593059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge20729ef-e6ae-4945-b868-b94238743262/dqc_reference/reference_markers.fasta -out GCA_025930595.1_ASM2593059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:53:56,497] [INFO] Task succeeded: Blastn
[2023-07-01 01:53:56,500] [INFO] Selected 20 target genomes.
[2023-07-01 01:53:56,501] [INFO] Target genome list was writen to GCA_025930595.1_ASM2593059v1_genomic.fna/target_genomes.txt
[2023-07-01 01:53:56,502] [INFO] Task started: fastANI
[2023-07-01 01:53:56,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b6c14ff-6e01-45cf-84b9-79f4683e115a/GCA_025930595.1_ASM2593059v1_genomic.fna.gz --refList GCA_025930595.1_ASM2593059v1_genomic.fna/target_genomes.txt --output GCA_025930595.1_ASM2593059v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:54:10,313] [INFO] Task succeeded: fastANI
[2023-07-01 01:54:10,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge20729ef-e6ae-4945-b868-b94238743262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:54:10,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge20729ef-e6ae-4945-b868-b94238743262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:54:10,329] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:54:10,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:54:10,329] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.8558	92	1077	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.8081	161	1077	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.5271	153	1077	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.3772	159	1077	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.3123	129	1077	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	75.2013	106	1077	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	75.1094	168	1077	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	75.018	110	1077	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	74.9829	56	1077	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.9802	75	1077	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	74.9478	202	1077	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	74.8916	207	1077	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	74.8864	209	1077	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	74.8599	59	1077	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	74.8483	124	1077	95	below_threshold
Actinoalloteichus cyanogriseus	strain=DSM 43889	GCA_000429185.2	65497	65497	type	True	74.8019	91	1077	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:54:10,331] [INFO] DFAST Taxonomy check result was written to GCA_025930595.1_ASM2593059v1_genomic.fna/tc_result.tsv
[2023-07-01 01:54:10,332] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:54:10,332] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:54:10,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge20729ef-e6ae-4945-b868-b94238743262/dqc_reference/checkm_data
[2023-07-01 01:54:10,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:54:10,378] [INFO] Task started: CheckM
[2023-07-01 01:54:10,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025930595.1_ASM2593059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025930595.1_ASM2593059v1_genomic.fna/checkm_input GCA_025930595.1_ASM2593059v1_genomic.fna/checkm_result
[2023-07-01 01:54:43,134] [INFO] Task succeeded: CheckM
[2023-07-01 01:54:43,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.14%
Contamintation: 8.02%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-07-01 01:54:43,161] [INFO] ===== Completeness check finished =====
[2023-07-01 01:54:43,162] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:54:43,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025930595.1_ASM2593059v1_genomic.fna/markers.fasta)
[2023-07-01 01:54:43,163] [INFO] Task started: Blastn
[2023-07-01 01:54:43,163] [INFO] Running command: blastn -query GCA_025930595.1_ASM2593059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge20729ef-e6ae-4945-b868-b94238743262/dqc_reference/reference_markers_gtdb.fasta -out GCA_025930595.1_ASM2593059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:54:44,000] [INFO] Task succeeded: Blastn
[2023-07-01 01:54:44,006] [INFO] Selected 22 target genomes.
[2023-07-01 01:54:44,006] [INFO] Target genome list was writen to GCA_025930595.1_ASM2593059v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:54:44,011] [INFO] Task started: fastANI
[2023-07-01 01:54:44,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b6c14ff-6e01-45cf-84b9-79f4683e115a/GCA_025930595.1_ASM2593059v1_genomic.fna.gz --refList GCA_025930595.1_ASM2593059v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025930595.1_ASM2593059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:54:55,772] [INFO] Task succeeded: fastANI
[2023-07-01 01:54:55,790] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 01:54:55,790] [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_013695115.1	s__JACDBD01 sp013695115	76.7906	107	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__JACDBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870395.1	s__SHUZ01 sp016870395	76.3794	105	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__IMCC26256;g__SHUZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870595.1	s__CAIUKV01 sp016870595	76.2578	125	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805665.1	s__CADCTB01 sp902805665	76.2488	147	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__CADCTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882925.1	s__Chersky-534 sp017882925	76.2329	134	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__Chersky-534;g__Chersky-534	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899845.1	s__CAIUKV01 sp903899845	76.2046	138	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	99.48	99.41	0.90	0.89	4	-
GCA_016870245.1	s__CAIUKV01 sp016870245	76.1735	153	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882945.1	s__Chersky-806 sp017882945	76.1669	87	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__IMCC26256;g__Chersky-806	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002861595.1	s__GCA-2861595 sp002861595	76.0599	103	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__GCA-2861595;g__GCA-2861595	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888325.1	s__AC-14 sp005888325	76.02	144	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__AC-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	75.952	192	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	75.894	142	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883065.1	s__Bog-756 sp017883065	75.8788	78	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	75.7532	61	1077	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_016845305.1	s__UBA9410 sp016845305	75.752	120	1077	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_009886115.1	s__VFJJ01 sp009886115	75.7054	140	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__VFJJ01;g__VFJJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140175.1	s__PALSA-555 sp003140175	75.6618	101	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__PALSA-555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	75.5088	126	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778215.1	s__UBA668 sp005778215	74.9816	69	1077	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.54	99.53	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-07-01 01:54:55,793] [INFO] GTDB search result was written to GCA_025930595.1_ASM2593059v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:54:55,793] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:54:55,797] [INFO] DFAST_QC result json was written to GCA_025930595.1_ASM2593059v1_genomic.fna/dqc_result.json
[2023-07-01 01:54:55,798] [INFO] DFAST_QC completed!
[2023-07-01 01:54:55,798] [INFO] Total running time: 0h1m11s