[2023-06-29 03:47:09,106] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:47:09,109] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:47:09,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e31566c-018f-4c43-9c10-4c97527d7f51/dqc_reference
[2023-06-29 03:47:10,433] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:47:10,434] [INFO] Task started: Prodigal
[2023-06-29 03:47:10,435] [INFO] Running command: gunzip -c /var/lib/cwl/stge1a61aea-cda3-4e1c-aec9-28d674b02602/GCA_015490905.1_ASM1549090v1_genomic.fna.gz | prodigal -d GCA_015490905.1_ASM1549090v1_genomic.fna/cds.fna -a GCA_015490905.1_ASM1549090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:47:19,077] [INFO] Task succeeded: Prodigal
[2023-06-29 03:47:19,078] [INFO] Task started: HMMsearch
[2023-06-29 03:47:19,078] [INFO] Running command: hmmsearch --tblout GCA_015490905.1_ASM1549090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e31566c-018f-4c43-9c10-4c97527d7f51/dqc_reference/reference_markers.hmm GCA_015490905.1_ASM1549090v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:47:19,324] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:47:19,326] [INFO] Found 6/6 markers.
[2023-06-29 03:47:19,355] [INFO] Query marker FASTA was written to GCA_015490905.1_ASM1549090v1_genomic.fna/markers.fasta
[2023-06-29 03:47:19,355] [INFO] Task started: Blastn
[2023-06-29 03:47:19,355] [INFO] Running command: blastn -query GCA_015490905.1_ASM1549090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e31566c-018f-4c43-9c10-4c97527d7f51/dqc_reference/reference_markers.fasta -out GCA_015490905.1_ASM1549090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:47:20,413] [INFO] Task succeeded: Blastn
[2023-06-29 03:47:20,417] [INFO] Selected 24 target genomes.
[2023-06-29 03:47:20,417] [INFO] Target genome list was writen to GCA_015490905.1_ASM1549090v1_genomic.fna/target_genomes.txt
[2023-06-29 03:47:20,420] [INFO] Task started: fastANI
[2023-06-29 03:47:20,420] [INFO] Running command: fastANI --query /var/lib/cwl/stge1a61aea-cda3-4e1c-aec9-28d674b02602/GCA_015490905.1_ASM1549090v1_genomic.fna.gz --refList GCA_015490905.1_ASM1549090v1_genomic.fna/target_genomes.txt --output GCA_015490905.1_ASM1549090v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:47:35,837] [INFO] Task succeeded: fastANI
[2023-06-29 03:47:35,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e31566c-018f-4c43-9c10-4c97527d7f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:47:35,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e31566c-018f-4c43-9c10-4c97527d7f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:47:35,861] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:47:35,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:47:35,861] [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
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	78.7278	285	916	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	78.5862	260	916	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	78.4392	275	916	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	78.2306	271	916	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.838	231	916	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	77.785	177	916	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	77.4977	185	916	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.4556	229	916	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	77.4307	182	916	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	77.4282	203	916	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	77.3825	178	916	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	77.3089	132	916	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.2982	222	916	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	77.2315	161	916	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.2168	225	916	95	below_threshold
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	77.1319	162	916	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	77.0863	154	916	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	77.0845	203	916	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.9017	199	916	95	below_threshold
Acidihalobacter ferrooxydans	strain=V8	GCA_001975725.1	1765967	1765967	type	True	76.7869	114	916	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.6043	175	916	95	below_threshold
Pseudomonas fluvialis	strain=ASS-1	GCA_002234375.1	1793966	1793966	suspected-type	True	76.5591	122	916	95	below_threshold
Pseudomonas fluvialis	strain=CCM 8778	GCA_014635625.1	1793966	1793966	suspected-type	True	76.4595	123	916	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.4507	104	916	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:47:35,873] [INFO] DFAST Taxonomy check result was written to GCA_015490905.1_ASM1549090v1_genomic.fna/tc_result.tsv
[2023-06-29 03:47:35,874] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:47:35,875] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:47:35,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e31566c-018f-4c43-9c10-4c97527d7f51/dqc_reference/checkm_data
[2023-06-29 03:47:35,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:47:35,918] [INFO] Task started: CheckM
[2023-06-29 03:47:35,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015490905.1_ASM1549090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015490905.1_ASM1549090v1_genomic.fna/checkm_input GCA_015490905.1_ASM1549090v1_genomic.fna/checkm_result
[2023-06-29 03:48:06,111] [INFO] Task succeeded: CheckM
[2023-06-29 03:48:06,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:48:06,150] [INFO] ===== Completeness check finished =====
[2023-06-29 03:48:06,150] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:48:06,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015490905.1_ASM1549090v1_genomic.fna/markers.fasta)
[2023-06-29 03:48:06,151] [INFO] Task started: Blastn
[2023-06-29 03:48:06,151] [INFO] Running command: blastn -query GCA_015490905.1_ASM1549090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e31566c-018f-4c43-9c10-4c97527d7f51/dqc_reference/reference_markers_gtdb.fasta -out GCA_015490905.1_ASM1549090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:48:08,295] [INFO] Task succeeded: Blastn
[2023-06-29 03:48:08,312] [INFO] Selected 19 target genomes.
[2023-06-29 03:48:08,313] [INFO] Target genome list was writen to GCA_015490905.1_ASM1549090v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:48:08,346] [INFO] Task started: fastANI
[2023-06-29 03:48:08,347] [INFO] Running command: fastANI --query /var/lib/cwl/stge1a61aea-cda3-4e1c-aec9-28d674b02602/GCA_015490905.1_ASM1549090v1_genomic.fna.gz --refList GCA_015490905.1_ASM1549090v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015490905.1_ASM1549090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:48:19,997] [INFO] Task succeeded: fastANI
[2023-06-29 03:48:20,019] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 03:48:20,020] [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_011371455.1	s__DRQN01 sp011371455	97.1963	533	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	conclusive
GCA_011051755.1	s__DRQN01 sp011051755	83.2972	643	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051685.1	s__SZUA-152 sp011051685	80.9057	359	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	78.7686	304	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	78.722	286	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	78.6022	259	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	78.5475	255	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	78.4677	273	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	78.4576	276	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	78.2446	270	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	78.1637	263	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	78.015	245	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	77.925	265	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151575.1	s__JAADHZ01 sp013151575	77.7033	204	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__JAADHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	77.401	242	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	77.313	226	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	77.2855	211	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355735.1	s__Sulfuricaulis limicola	77.1319	162	916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:48:20,022] [INFO] GTDB search result was written to GCA_015490905.1_ASM1549090v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:48:20,022] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:48:20,029] [INFO] DFAST_QC result json was written to GCA_015490905.1_ASM1549090v1_genomic.fna/dqc_result.json
[2023-06-29 03:48:20,030] [INFO] DFAST_QC completed!
[2023-06-29 03:48:20,030] [INFO] Total running time: 0h1m11s