[2024-01-24 11:26:20,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a6b59ad-d679-436d-893b-b478da672817/dqc_reference
[2024-01-24 11:26:21,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:21,913] [INFO] Task started: Prodigal
[2024-01-24 11:26:21,913] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6e0a59d-4838-432d-aa4b-53c0727687c1/GCF_002924445.1_ASM292444v1_genomic.fna.gz | prodigal -d GCF_002924445.1_ASM292444v1_genomic.fna/cds.fna -a GCF_002924445.1_ASM292444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:34,886] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:34,886] [INFO] Task started: HMMsearch
[2024-01-24 11:26:34,887] [INFO] Running command: hmmsearch --tblout GCF_002924445.1_ASM292444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a6b59ad-d679-436d-893b-b478da672817/dqc_reference/reference_markers.hmm GCF_002924445.1_ASM292444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:35,250] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:35,252] [INFO] Found 6/6 markers.
[2024-01-24 11:26:35,298] [INFO] Query marker FASTA was written to GCF_002924445.1_ASM292444v1_genomic.fna/markers.fasta
[2024-01-24 11:26:35,299] [INFO] Task started: Blastn
[2024-01-24 11:26:35,299] [INFO] Running command: blastn -query GCF_002924445.1_ASM292444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a6b59ad-d679-436d-893b-b478da672817/dqc_reference/reference_markers.fasta -out GCF_002924445.1_ASM292444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:36,320] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:36,323] [INFO] Selected 29 target genomes.
[2024-01-24 11:26:36,324] [INFO] Target genome list was writen to GCF_002924445.1_ASM292444v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:36,338] [INFO] Task started: fastANI
[2024-01-24 11:26:36,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6e0a59d-4838-432d-aa4b-53c0727687c1/GCF_002924445.1_ASM292444v1_genomic.fna.gz --refList GCF_002924445.1_ASM292444v1_genomic.fna/target_genomes.txt --output GCF_002924445.1_ASM292444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:03,422] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:03,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a6b59ad-d679-436d-893b-b478da672817/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:03,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a6b59ad-d679-436d-893b-b478da672817/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:03,447] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:03,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:03,447] [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
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	100.0	1567	1589	95	conclusive
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.169	476	1589	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.1457	474	1589	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.1385	415	1589	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	77.0948	357	1589	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.0732	313	1589	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	76.8208	232	1589	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.6817	300	1589	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6527	393	1589	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.6288	404	1589	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	76.6198	255	1589	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	76.6051	164	1589	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.5884	213	1589	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.578	298	1589	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.5393	226	1589	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.4833	284	1589	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.4583	342	1589	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	76.4562	277	1589	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.4408	307	1589	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.3804	194	1589	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.3757	260	1589	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	76.3239	217	1589	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.3184	309	1589	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	76.2652	202	1589	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	76.2025	328	1589	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1935	230	1589	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	76.1507	329	1589	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	76.1163	283	1589	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.6331	235	1589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:03,449] [INFO] DFAST Taxonomy check result was written to GCF_002924445.1_ASM292444v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:03,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:03,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:03,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a6b59ad-d679-436d-893b-b478da672817/dqc_reference/checkm_data
[2024-01-24 11:27:03,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:03,497] [INFO] Task started: CheckM
[2024-01-24 11:27:03,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002924445.1_ASM292444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002924445.1_ASM292444v1_genomic.fna/checkm_input GCF_002924445.1_ASM292444v1_genomic.fna/checkm_result
[2024-01-24 11:27:45,288] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:45,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:45,312] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:45,312] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:45,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002924445.1_ASM292444v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:45,313] [INFO] Task started: Blastn
[2024-01-24 11:27:45,313] [INFO] Running command: blastn -query GCF_002924445.1_ASM292444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a6b59ad-d679-436d-893b-b478da672817/dqc_reference/reference_markers_gtdb.fasta -out GCF_002924445.1_ASM292444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:47,289] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:47,293] [INFO] Selected 24 target genomes.
[2024-01-24 11:27:47,294] [INFO] Target genome list was writen to GCF_002924445.1_ASM292444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:47,321] [INFO] Task started: fastANI
[2024-01-24 11:27:47,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6e0a59d-4838-432d-aa4b-53c0727687c1/GCF_002924445.1_ASM292444v1_genomic.fna.gz --refList GCF_002924445.1_ASM292444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002924445.1_ASM292444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:10,984] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:11,006] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:11,006] [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_002924445.1	s__Minwuia thermotolerans	100.0	1566	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	conclusive
GCA_016865035.1	s__Minwuia sp016865035	78.5753	623	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.1122	477	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008728835.1	s__Hypericibacter adhaerens	77.0722	314	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	77.0684	358	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	76.8166	310	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	76.6651	392	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	76.6497	281	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.5543	403	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	76.5476	296	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131015.1	s__Bradyrhizobium diazoefficiens_B	76.4753	282	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.4514	345	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	76.4433	279	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCA_016870055.1	s__Reyranella sp016870055	76.4138	253	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205765.1	s__Nitrospirillum iridis	76.3711	262	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	76.3404	293	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070395.1	s__CLL3-39 sp012070395	76.2854	205	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CLL3-39	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001458395.1	s__Leisingera aquaemixtae	76.2788	182	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_001687105.1	s__Salipiger sp001687105	76.261	187	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_007828035.1	s__Nitrospirillum amazonense_A	76.2193	255	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222815.1	s__Roseomonas_A sp005222815	76.2001	314	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802185.1	s__Belnapia sp000802185	76.1628	286	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	76.1121	310	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009712185.1	s__Telmatospirillum sp009712185	76.0165	185	1589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:11,008] [INFO] GTDB search result was written to GCF_002924445.1_ASM292444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:11,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:11,013] [INFO] DFAST_QC result json was written to GCF_002924445.1_ASM292444v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:11,014] [INFO] DFAST_QC completed!
[2024-01-24 11:28:11,014] [INFO] Total running time: 0h1m50s