[2023-06-18 11:44:54,622] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:44:54,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:44:54,626] [INFO] DQC Reference Directory: /var/lib/cwl/stga8b0fa1c-431f-45ac-9e83-950856ed0959/dqc_reference
[2023-06-18 11:44:57,947] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:44:57,948] [INFO] Task started: Prodigal
[2023-06-18 11:44:57,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg776b0fcc-e7d7-4273-b887-6e93e45a49ba/GCA_018268545.1_ASM1826854v1_genomic.fna.gz | prodigal -d GCA_018268545.1_ASM1826854v1_genomic.fna/cds.fna -a GCA_018268545.1_ASM1826854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:45:04,812] [INFO] Task succeeded: Prodigal
[2023-06-18 11:45:04,813] [INFO] Task started: HMMsearch
[2023-06-18 11:45:04,813] [INFO] Running command: hmmsearch --tblout GCA_018268545.1_ASM1826854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8b0fa1c-431f-45ac-9e83-950856ed0959/dqc_reference/reference_markers.hmm GCA_018268545.1_ASM1826854v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:45:05,037] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:45:05,039] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg776b0fcc-e7d7-4273-b887-6e93e45a49ba/GCA_018268545.1_ASM1826854v1_genomic.fna.gz]
[2023-06-18 11:45:05,072] [INFO] Query marker FASTA was written to GCA_018268545.1_ASM1826854v1_genomic.fna/markers.fasta
[2023-06-18 11:45:05,072] [INFO] Task started: Blastn
[2023-06-18 11:45:05,072] [INFO] Running command: blastn -query GCA_018268545.1_ASM1826854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8b0fa1c-431f-45ac-9e83-950856ed0959/dqc_reference/reference_markers.fasta -out GCA_018268545.1_ASM1826854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:45:05,769] [INFO] Task succeeded: Blastn
[2023-06-18 11:45:05,774] [INFO] Selected 13 target genomes.
[2023-06-18 11:45:05,774] [INFO] Target genome list was writen to GCA_018268545.1_ASM1826854v1_genomic.fna/target_genomes.txt
[2023-06-18 11:45:05,778] [INFO] Task started: fastANI
[2023-06-18 11:45:05,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg776b0fcc-e7d7-4273-b887-6e93e45a49ba/GCA_018268545.1_ASM1826854v1_genomic.fna.gz --refList GCA_018268545.1_ASM1826854v1_genomic.fna/target_genomes.txt --output GCA_018268545.1_ASM1826854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:45:15,020] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:15,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8b0fa1c-431f-45ac-9e83-950856ed0959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:45:15,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8b0fa1c-431f-45ac-9e83-950856ed0959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:45:15,033] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:45:15,033] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:45:15,034] [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	76.5766	81	677	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.47	104	677	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.3878	114	677	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.0433	82	677	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.6785	111	677	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.4602	92	677	95	below_threshold
Amycolatopsis jiangsuensis	strain=DSM 45859	GCA_014204865.1	1181879	1181879	type	True	75.2849	71	677	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	75.1492	81	677	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	75.1147	72	677	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:45:15,035] [INFO] DFAST Taxonomy check result was written to GCA_018268545.1_ASM1826854v1_genomic.fna/tc_result.tsv
[2023-06-18 11:45:15,036] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:45:15,036] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:45:15,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8b0fa1c-431f-45ac-9e83-950856ed0959/dqc_reference/checkm_data
[2023-06-18 11:45:15,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:45:15,068] [INFO] Task started: CheckM
[2023-06-18 11:45:15,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018268545.1_ASM1826854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018268545.1_ASM1826854v1_genomic.fna/checkm_input GCA_018268545.1_ASM1826854v1_genomic.fna/checkm_result
[2023-06-18 11:45:53,791] [INFO] Task succeeded: CheckM
[2023-06-18 11:45:53,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:45:53,810] [INFO] ===== Completeness check finished =====
[2023-06-18 11:45:53,810] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:45:53,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018268545.1_ASM1826854v1_genomic.fna/markers.fasta)
[2023-06-18 11:45:53,811] [INFO] Task started: Blastn
[2023-06-18 11:45:53,811] [INFO] Running command: blastn -query GCA_018268545.1_ASM1826854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8b0fa1c-431f-45ac-9e83-950856ed0959/dqc_reference/reference_markers_gtdb.fasta -out GCA_018268545.1_ASM1826854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:45:54,797] [INFO] Task succeeded: Blastn
[2023-06-18 11:45:54,801] [INFO] Selected 17 target genomes.
[2023-06-18 11:45:54,802] [INFO] Target genome list was writen to GCA_018268545.1_ASM1826854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:45:54,813] [INFO] Task started: fastANI
[2023-06-18 11:45:54,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg776b0fcc-e7d7-4273-b887-6e93e45a49ba/GCA_018268545.1_ASM1826854v1_genomic.fna.gz --refList GCA_018268545.1_ASM1826854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018268545.1_ASM1826854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:46:03,603] [INFO] Task succeeded: fastANI
[2023-06-18 11:46:03,620] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:46:03,621] [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_018268545.1	s__JAFDWI01 sp018268545	100.0	669	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAFDWI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017882935.1	s__JADGOP01 sp017882935	76.6714	107	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JADGOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	76.4623	79	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268735.1	s__AWTP1-35 sp018268735	76.3103	69	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.2847	116	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	76.1971	80	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247975.1	s__JAFBAD01 sp019247975	76.1164	78	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAFBAD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.1012	116	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.0866	74	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_012513855.1	s__JAAZBK01 sp012513855	76.0465	77	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	76.0291	109	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	76.0261	116	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962875.1	s__AWTP1-35 sp003962875	75.9756	97	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781105.1	s__JADDRA01 sp016781105	75.8751	54	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__JADDRA01	95.0	99.25	99.25	0.80	0.80	2	-
GCA_016870245.1	s__CAIUKV01 sp016870245	75.841	87	677	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_903899845.1	s__CAIUKV01 sp903899845	75.717	92	677	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_903921205.1	s__CAIXPF01 sp903921205	75.3356	78	677	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__CAIXPF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:46:03,623] [INFO] GTDB search result was written to GCA_018268545.1_ASM1826854v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:46:03,623] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:46:03,627] [INFO] DFAST_QC result json was written to GCA_018268545.1_ASM1826854v1_genomic.fna/dqc_result.json
[2023-06-18 11:46:03,627] [INFO] DFAST_QC completed!
[2023-06-18 11:46:03,628] [INFO] Total running time: 0h1m9s