[2024-01-24 11:34:38,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg4138ec54-2bbf-409f-b18d-184c5724ccf5/dqc_reference
[2024-01-24 11:34:41,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,324] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,325] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8301377-d0ea-4ede-a882-0df0a0549956/GCF_006385175.1_ASM638517v1_genomic.fna.gz | prodigal -d GCF_006385175.1_ASM638517v1_genomic.fna/cds.fna -a GCF_006385175.1_ASM638517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,327] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,328] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,328] [INFO] Running command: hmmsearch --tblout GCF_006385175.1_ASM638517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4138ec54-2bbf-409f-b18d-184c5724ccf5/dqc_reference/reference_markers.hmm GCF_006385175.1_ASM638517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,610] [INFO] Found 6/6 markers.
[2024-01-24 11:34:53,651] [INFO] Query marker FASTA was written to GCF_006385175.1_ASM638517v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,651] [INFO] Task started: Blastn
[2024-01-24 11:34:53,651] [INFO] Running command: blastn -query GCF_006385175.1_ASM638517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4138ec54-2bbf-409f-b18d-184c5724ccf5/dqc_reference/reference_markers.fasta -out GCF_006385175.1_ASM638517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,431] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,434] [INFO] Selected 26 target genomes.
[2024-01-24 11:34:54,435] [INFO] Target genome list was writen to GCF_006385175.1_ASM638517v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,445] [INFO] Task started: fastANI
[2024-01-24 11:34:54,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8301377-d0ea-4ede-a882-0df0a0549956/GCF_006385175.1_ASM638517v1_genomic.fna.gz --refList GCF_006385175.1_ASM638517v1_genomic.fna/target_genomes.txt --output GCF_006385175.1_ASM638517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:12,975] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:12,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4138ec54-2bbf-409f-b18d-184c5724ccf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:12,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4138ec54-2bbf-409f-b18d-184c5724ccf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:12,993] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:12,993] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:12,994] [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
Emcibacter nanhaiensis	strain=MCCC 1A06723	GCA_006385175.1	1505037	1505037	type	True	100.0	1304	1309	95	conclusive
Luteithermobacter gelatinilyticus	strain=MEBiC09520	GCA_005849285.1	2582913	2582913	type	True	77.948	350	1309	95	below_threshold
Paremcibacter congregatus	strain=ZYLT	GCA_006385135.1	2043170	2043170	type	True	77.2265	203	1309	95	below_threshold
Paremcibacter congregatus	strain=ZYL	GCA_002740695.1	2043170	2043170	type	True	77.1523	208	1309	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	76.9173	110	1309	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	76.8026	55	1309	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.7619	71	1309	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.6823	71	1309	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5606	90	1309	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.5285	90	1309	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.5278	119	1309	95	below_threshold
Eilatimonas milleporae	strain=DSM 25217	GCA_003688555.1	911205	911205	type	True	76.4074	83	1309	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.2252	58	1309	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.1933	132	1309	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	76.19	52	1309	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	76.0612	77	1309	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.0041	73	1309	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	76.0035	61	1309	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	75.9827	58	1309	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.6515	92	1309	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.3838	87	1309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:12,996] [INFO] DFAST Taxonomy check result was written to GCF_006385175.1_ASM638517v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:13,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:13,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:13,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4138ec54-2bbf-409f-b18d-184c5724ccf5/dqc_reference/checkm_data
[2024-01-24 11:35:13,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:13,049] [INFO] Task started: CheckM
[2024-01-24 11:35:13,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385175.1_ASM638517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385175.1_ASM638517v1_genomic.fna/checkm_input GCF_006385175.1_ASM638517v1_genomic.fna/checkm_result
[2024-01-24 11:35:51,436] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:51,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:51,455] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:51,456] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:51,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385175.1_ASM638517v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:51,457] [INFO] Task started: Blastn
[2024-01-24 11:35:51,457] [INFO] Running command: blastn -query GCF_006385175.1_ASM638517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4138ec54-2bbf-409f-b18d-184c5724ccf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385175.1_ASM638517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:52,946] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:52,950] [INFO] Selected 24 target genomes.
[2024-01-24 11:35:52,950] [INFO] Target genome list was writen to GCF_006385175.1_ASM638517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:52,978] [INFO] Task started: fastANI
[2024-01-24 11:35:52,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8301377-d0ea-4ede-a882-0df0a0549956/GCF_006385175.1_ASM638517v1_genomic.fna.gz --refList GCF_006385175.1_ASM638517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385175.1_ASM638517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:09,971] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:09,993] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:09,993] [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_006385175.1	s__Emcibacter nanhaiensis	100.0	1305	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Emcibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005849285.1	s__Luteithermobacter gelatinilyticus	77.8988	349	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Luteithermobacter	95.0	99.04	99.04	0.96	0.96	2	-
GCF_006385135.1	s__Paremcibacter congregatus	77.3036	204	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009882935.1	s__Sneathiella chungangensis	76.7764	69	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003233655.1	s__Azospirillum ramasamyi	76.549	118	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688555.1	s__Eilatimonas milleporae	76.4074	83	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Eilatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051815.1	s__Paremcibacter sp011051815	76.3476	89	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	76.3345	144	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCF_000333275.1	s__Nitrospirillum sp000333275	76.2671	114	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401545.1	s__Paremcibacter sp002401545	76.2618	89	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002749135.1	s__Paremcibacter sp002749135	76.2221	123	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205765.1	s__Nitrospirillum iridis	76.1877	131	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	76.0035	61	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744315.1	s__Croceibacterium sp017744315	75.9651	51	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595235.1	s__Nordella sp016595235	75.8498	74	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.8301	109	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012315.1	s__SSEL01 sp008012315	75.672	93	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SSEL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:09,995] [INFO] GTDB search result was written to GCF_006385175.1_ASM638517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:09,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:10,002] [INFO] DFAST_QC result json was written to GCF_006385175.1_ASM638517v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:10,002] [INFO] DFAST_QC completed!
[2024-01-24 11:36:10,003] [INFO] Total running time: 0h1m31s