[2024-01-25 18:03:50,843] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:50,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:50,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a4cb100-8a13-4c07-8f06-b2f0aa76c5c2/dqc_reference
[2024-01-25 18:03:51,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:51,982] [INFO] Task started: Prodigal
[2024-01-25 18:03:51,982] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe458dfc-27db-4da7-8e3f-0e105c0896ae/GCF_001005215.1_ASM100521v1_genomic.fna.gz | prodigal -d GCF_001005215.1_ASM100521v1_genomic.fna/cds.fna -a GCF_001005215.1_ASM100521v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:01,690] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:01,691] [INFO] Task started: HMMsearch
[2024-01-25 18:04:01,691] [INFO] Running command: hmmsearch --tblout GCF_001005215.1_ASM100521v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a4cb100-8a13-4c07-8f06-b2f0aa76c5c2/dqc_reference/reference_markers.hmm GCF_001005215.1_ASM100521v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:01,917] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:01,919] [INFO] Found 6/6 markers.
[2024-01-25 18:04:01,945] [INFO] Query marker FASTA was written to GCF_001005215.1_ASM100521v1_genomic.fna/markers.fasta
[2024-01-25 18:04:01,945] [INFO] Task started: Blastn
[2024-01-25 18:04:01,945] [INFO] Running command: blastn -query GCF_001005215.1_ASM100521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4cb100-8a13-4c07-8f06-b2f0aa76c5c2/dqc_reference/reference_markers.fasta -out GCF_001005215.1_ASM100521v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:02,838] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:02,842] [INFO] Selected 22 target genomes.
[2024-01-25 18:04:02,842] [INFO] Target genome list was writen to GCF_001005215.1_ASM100521v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:02,856] [INFO] Task started: fastANI
[2024-01-25 18:04:02,856] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe458dfc-27db-4da7-8e3f-0e105c0896ae/GCF_001005215.1_ASM100521v1_genomic.fna.gz --refList GCF_001005215.1_ASM100521v1_genomic.fna/target_genomes.txt --output GCF_001005215.1_ASM100521v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:23,081] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:23,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a4cb100-8a13-4c07-8f06-b2f0aa76c5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:23,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a4cb100-8a13-4c07-8f06-b2f0aa76c5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:23,096] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:04:23,096] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:04:23,096] [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
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	80.1362	275	1032	95	below_threshold
Corticibacter populi	strain=DSM 105136	GCA_004217315.1	1550736	1550736	type	True	80.1109	543	1032	95	below_threshold
Corticibacter populi	strain=DSM 105136	GCA_003703815.1	1550736	1550736	type	True	80.1107	545	1032	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	78.8449	359	1032	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.6999	372	1032	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	78.1916	318	1032	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	78.1871	295	1032	95	below_threshold
Lampropedia hyalina	strain=DSM 16112	GCA_900129055.1	198706	198706	type	True	78.0707	317	1032	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.0431	290	1032	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	78.0308	299	1032	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	78.0295	282	1032	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	78.0131	307	1032	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	77.9101	253	1032	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	77.8939	343	1032	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.8684	279	1032	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	77.7863	245	1032	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	77.7091	284	1032	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.4634	272	1032	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	77.4049	274	1032	95	below_threshold
Lampropedia aestuarii	strain=YIM MLB12	GCA_004803635.1	2562762	2562762	type	True	77.3591	246	1032	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.3512	212	1032	95	below_threshold
Lampropedia puyangensis	strain=2-bin	GCA_004833285.1	1330072	1330072	type	True	77.194	161	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:23,098] [INFO] DFAST Taxonomy check result was written to GCF_001005215.1_ASM100521v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:23,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:23,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:23,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a4cb100-8a13-4c07-8f06-b2f0aa76c5c2/dqc_reference/checkm_data
[2024-01-25 18:04:23,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:23,137] [INFO] Task started: CheckM
[2024-01-25 18:04:23,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001005215.1_ASM100521v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001005215.1_ASM100521v1_genomic.fna/checkm_input GCF_001005215.1_ASM100521v1_genomic.fna/checkm_result
[2024-01-25 18:04:57,858] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:57,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:57,914] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:57,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:57,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001005215.1_ASM100521v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:57,915] [INFO] Task started: Blastn
[2024-01-25 18:04:57,915] [INFO] Running command: blastn -query GCF_001005215.1_ASM100521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4cb100-8a13-4c07-8f06-b2f0aa76c5c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001005215.1_ASM100521v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:59,779] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:59,782] [INFO] Selected 12 target genomes.
[2024-01-25 18:04:59,782] [INFO] Target genome list was writen to GCF_001005215.1_ASM100521v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:59,794] [INFO] Task started: fastANI
[2024-01-25 18:04:59,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe458dfc-27db-4da7-8e3f-0e105c0896ae/GCF_001005215.1_ASM100521v1_genomic.fna.gz --refList GCF_001005215.1_ASM100521v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001005215.1_ASM100521v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:09,136] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:09,144] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:09,144] [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
GCF_001005215.1	s__Lampropedia cohaerens	100.0	1027	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217315.1	s__Lampropedia populi	80.1273	541	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002285265.1	s__Lampropedia sp002285265	80.0707	457	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	96.24	95.49	0.89	0.89	3	-
GCA_002285285.1	s__Lampropedia sp002285285	79.7346	432	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	97.35	97.22	0.92	0.90	6	-
GCA_003703475.1	s__Lampropedia sp003703475	78.9694	335	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	98.05	97.54	0.92	0.91	4	-
GCA_018240985.1	s__Alicycliphilus sp018240985	78.3098	280	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCA_013693755.1	s__Tibeticola sp013693755	78.1627	277	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_014076495.1	s__Comamonas koreensis	77.9046	287	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.44	95.11	0.92	0.89	4	-
GCA_011772445.1	s__Hydrogenophaga sp011772445	77.7995	252	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	9	-
GCA_000426125.1	s__Ramlibacter sp000426125	77.6707	247	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803635.1	s__Lampropedia aestuarii	77.3709	245	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012274225.1	s__Ramlibacter sp012274225	77.1245	179	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:09,146] [INFO] GTDB search result was written to GCF_001005215.1_ASM100521v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:09,146] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:09,150] [INFO] DFAST_QC result json was written to GCF_001005215.1_ASM100521v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:09,151] [INFO] DFAST_QC completed!
[2024-01-25 18:05:09,151] [INFO] Total running time: 0h1m18s