[2024-01-24 14:07:00,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:00,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:00,433] [INFO] DQC Reference Directory: /var/lib/cwl/stge6fc8069-8a8e-429c-91d6-222f22be3b45/dqc_reference
[2024-01-24 14:07:01,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:01,818] [INFO] Task started: Prodigal
[2024-01-24 14:07:01,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3127e75-24c1-4806-a782-90d94a26b4b0/GCF_003572205.1_ASM357220v1_genomic.fna.gz | prodigal -d GCF_003572205.1_ASM357220v1_genomic.fna/cds.fna -a GCF_003572205.1_ASM357220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:14,851] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:14,851] [INFO] Task started: HMMsearch
[2024-01-24 14:07:14,851] [INFO] Running command: hmmsearch --tblout GCF_003572205.1_ASM357220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6fc8069-8a8e-429c-91d6-222f22be3b45/dqc_reference/reference_markers.hmm GCF_003572205.1_ASM357220v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:15,081] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:15,082] [INFO] Found 6/6 markers.
[2024-01-24 14:07:15,120] [INFO] Query marker FASTA was written to GCF_003572205.1_ASM357220v1_genomic.fna/markers.fasta
[2024-01-24 14:07:15,120] [INFO] Task started: Blastn
[2024-01-24 14:07:15,120] [INFO] Running command: blastn -query GCF_003572205.1_ASM357220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6fc8069-8a8e-429c-91d6-222f22be3b45/dqc_reference/reference_markers.fasta -out GCF_003572205.1_ASM357220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:15,936] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:15,940] [INFO] Selected 21 target genomes.
[2024-01-24 14:07:15,940] [INFO] Target genome list was writen to GCF_003572205.1_ASM357220v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:15,949] [INFO] Task started: fastANI
[2024-01-24 14:07:15,950] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3127e75-24c1-4806-a782-90d94a26b4b0/GCF_003572205.1_ASM357220v1_genomic.fna.gz --refList GCF_003572205.1_ASM357220v1_genomic.fna/target_genomes.txt --output GCF_003572205.1_ASM357220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:35,066] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:35,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6fc8069-8a8e-429c-91d6-222f22be3b45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:35,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6fc8069-8a8e-429c-91d6-222f22be3b45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:35,082] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:35,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:35,082] [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
Algihabitans albus	strain=HHTR 118	GCA_003572205.1	2164067	2164067	type	True	100.0	1549	1552	95	conclusive
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	78.2523	474	1552	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	78.2293	480	1552	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.6556	341	1552	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.8833	212	1552	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.8759	219	1552	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.7698	230	1552	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.7321	173	1552	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	76.717	208	1552	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.7043	206	1552	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.6319	254	1552	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.5678	166	1552	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.4993	268	1552	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.3787	178	1552	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.294	246	1552	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	76.1783	136	1552	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.1537	158	1552	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.0933	131	1552	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	76.0845	105	1552	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.0237	184	1552	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.0002	143	1552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:35,084] [INFO] DFAST Taxonomy check result was written to GCF_003572205.1_ASM357220v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:35,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:35,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:35,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6fc8069-8a8e-429c-91d6-222f22be3b45/dqc_reference/checkm_data
[2024-01-24 14:07:35,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:35,129] [INFO] Task started: CheckM
[2024-01-24 14:07:35,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003572205.1_ASM357220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003572205.1_ASM357220v1_genomic.fna/checkm_input GCF_003572205.1_ASM357220v1_genomic.fna/checkm_result
[2024-01-24 14:08:13,983] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:13,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:14,004] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:14,004] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:14,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003572205.1_ASM357220v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:14,005] [INFO] Task started: Blastn
[2024-01-24 14:08:14,005] [INFO] Running command: blastn -query GCF_003572205.1_ASM357220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6fc8069-8a8e-429c-91d6-222f22be3b45/dqc_reference/reference_markers_gtdb.fasta -out GCF_003572205.1_ASM357220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:15,508] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:15,512] [INFO] Selected 19 target genomes.
[2024-01-24 14:08:15,512] [INFO] Target genome list was writen to GCF_003572205.1_ASM357220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:15,524] [INFO] Task started: fastANI
[2024-01-24 14:08:15,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3127e75-24c1-4806-a782-90d94a26b4b0/GCF_003572205.1_ASM357220v1_genomic.fna.gz --refList GCF_003572205.1_ASM357220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003572205.1_ASM357220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:31,741] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:31,756] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:31,757] [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_003572205.1	s__Algihabitans albus	100.0	1549	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001637315.1	s__Phormidium_A willei_A	80.7285	70	1552	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	95.56	95.56	0.82	0.82	2	-
GCA_006969625.1	s__Algihabitans sp006969625	80.255	754	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	78.237	479	1552	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_014925385.1	s__WHTV01 sp014925385	77.6371	343	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	77.3504	316	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	77.2609	309	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	77.1206	241	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	77.0756	241	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_016653635.2	s__Skermanella sp016653635	76.8969	249	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515255.1	s__Rhodovibrio salinarum	76.8944	211	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.7323	281	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.7046	207	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017963645.1	s__Marivibrio halodurans	76.5933	164	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Marivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869975.1	s__JAFAZJ01 sp016869975	76.5207	188	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.5013	193	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792605.1	s__JAEULC01 sp016792605	76.33	191	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULC01;f__JAEULC01;g__JAEULC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992075.1	s__Pararhodospirillum oryzae	76.0993	104	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667335.1	s__UBA8079 sp018667335	76.0917	98	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:31,758] [INFO] GTDB search result was written to GCF_003572205.1_ASM357220v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:31,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:31,763] [INFO] DFAST_QC result json was written to GCF_003572205.1_ASM357220v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:31,763] [INFO] DFAST_QC completed!
[2024-01-24 14:08:31,763] [INFO] Total running time: 0h1m31s