[2024-01-24 12:15:18,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,829] [INFO] DQC Reference Directory: /var/lib/cwl/stgb74ccdfb-ebb7-4c73-8538-47036048b589/dqc_reference
[2024-01-24 12:15:20,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,066] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,066] [INFO] Running command: gunzip -c /var/lib/cwl/stgf251ff88-2709-4440-8a97-19f716c220ee/GCF_019800005.1_ASM1980000v1_genomic.fna.gz | prodigal -d GCF_019800005.1_ASM1980000v1_genomic.fna/cds.fna -a GCF_019800005.1_ASM1980000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:36,532] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:36,533] [INFO] Task started: HMMsearch
[2024-01-24 12:15:36,533] [INFO] Running command: hmmsearch --tblout GCF_019800005.1_ASM1980000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb74ccdfb-ebb7-4c73-8538-47036048b589/dqc_reference/reference_markers.hmm GCF_019800005.1_ASM1980000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:36,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:36,855] [INFO] Found 6/6 markers.
[2024-01-24 12:15:36,904] [INFO] Query marker FASTA was written to GCF_019800005.1_ASM1980000v1_genomic.fna/markers.fasta
[2024-01-24 12:15:36,904] [INFO] Task started: Blastn
[2024-01-24 12:15:36,905] [INFO] Running command: blastn -query GCF_019800005.1_ASM1980000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb74ccdfb-ebb7-4c73-8538-47036048b589/dqc_reference/reference_markers.fasta -out GCF_019800005.1_ASM1980000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:37,832] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:37,840] [INFO] Selected 28 target genomes.
[2024-01-24 12:15:37,841] [INFO] Target genome list was writen to GCF_019800005.1_ASM1980000v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:37,851] [INFO] Task started: fastANI
[2024-01-24 12:15:37,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgf251ff88-2709-4440-8a97-19f716c220ee/GCF_019800005.1_ASM1980000v1_genomic.fna.gz --refList GCF_019800005.1_ASM1980000v1_genomic.fna/target_genomes.txt --output GCF_019800005.1_ASM1980000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:02,306] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:02,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb74ccdfb-ebb7-4c73-8538-47036048b589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:02,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb74ccdfb-ebb7-4c73-8538-47036048b589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:02,333] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:16:02,333] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:16:02,333] [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
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	83.9917	1301	1852	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.7576	429	1852	95	below_threshold
Arboricoccus pini	strain=B29T1	GCA_900187945.1	1963835	1963835	type	True	76.7258	188	1852	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.6935	195	1852	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.622	291	1852	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.6036	370	1852	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.55	419	1852	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.5006	245	1852	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.497	491	1852	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.4928	218	1852	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.4513	492	1852	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	76.4444	209	1852	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	76.4186	236	1852	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	76.3714	285	1852	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	76.3666	220	1852	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.3645	264	1852	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	76.3495	247	1852	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.3341	252	1852	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.3299	396	1852	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.2802	291	1852	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.2584	230	1852	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	76.1813	166	1852	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.1714	299	1852	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	76.1489	164	1852	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.097	372	1852	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.096	330	1852	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.0959	270	1852	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	75.9694	148	1852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:02,336] [INFO] DFAST Taxonomy check result was written to GCF_019800005.1_ASM1980000v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:02,337] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:02,337] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:02,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb74ccdfb-ebb7-4c73-8538-47036048b589/dqc_reference/checkm_data
[2024-01-24 12:16:02,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:02,398] [INFO] Task started: CheckM
[2024-01-24 12:16:02,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019800005.1_ASM1980000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019800005.1_ASM1980000v1_genomic.fna/checkm_input GCF_019800005.1_ASM1980000v1_genomic.fna/checkm_result
[2024-01-24 12:16:56,687] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:56,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:56,719] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:56,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:56,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019800005.1_ASM1980000v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:56,720] [INFO] Task started: Blastn
[2024-01-24 12:16:56,720] [INFO] Running command: blastn -query GCF_019800005.1_ASM1980000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb74ccdfb-ebb7-4c73-8538-47036048b589/dqc_reference/reference_markers_gtdb.fasta -out GCF_019800005.1_ASM1980000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:58,464] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:58,468] [INFO] Selected 26 target genomes.
[2024-01-24 12:16:58,469] [INFO] Target genome list was writen to GCF_019800005.1_ASM1980000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:58,498] [INFO] Task started: fastANI
[2024-01-24 12:16:58,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgf251ff88-2709-4440-8a97-19f716c220ee/GCF_019800005.1_ASM1980000v1_genomic.fna.gz --refList GCF_019800005.1_ASM1980000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019800005.1_ASM1980000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:20,135] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:20,167] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:17:20,167] [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_000427665.1	s__Geminicoccus roseus	84.007	1298	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Geminicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131045.1	s__SLRI01 sp007131045	77.5694	265	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826935.1	s__CADEGR01 sp902826935	77.34	437	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
GCA_011390475.1	s__SLRI01 sp011390475	77.2272	282	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908425.1	s__JAAAPF01 sp009908425	77.0118	245	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__JAAAPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187945.1	s__Arboricoccus pini	76.6918	191	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Arboricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336875.1	s__Oleisolibacter albus	76.5871	280	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	76.5431	240	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCF_003130795.1	s__Azospirillum thermophilum	76.5239	420	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490605.1	s__HRBIN39 sp015490605	76.4711	171	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__HRBIN39	95.0	97.05	97.05	0.84	0.84	2	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.4701	317	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003116015.1	s__Azospirillum sp003116015	76.4598	448	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312425.1	s__Reyranella massiliensis	76.4022	238	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308495.1	s__Afipia sp017308495	76.3871	173	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350535.1	s__Microvirga subterranea	76.3432	248	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	76.3364	238	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	76.3257	397	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	76.2799	288	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	76.2785	310	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	76.1882	320	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	76.1564	190	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001939945.1	s__Aerophototrophica crusticola	76.1561	321	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Aerophototrophica	95.0	99.94	99.94	0.97	0.97	2	-
GCA_016869645.1	s__SHVW01 sp016869645	76.139	265	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	76.1137	328	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870055.1	s__Reyranella sp016870055	76.0897	235	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019235415.1	s__Reyranella sp019235415	75.991	269	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.35	99.35	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:20,169] [INFO] GTDB search result was written to GCF_019800005.1_ASM1980000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:20,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:20,175] [INFO] DFAST_QC result json was written to GCF_019800005.1_ASM1980000v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:20,175] [INFO] DFAST_QC completed!
[2024-01-24 12:17:20,176] [INFO] Total running time: 0h2m1s