[2024-01-24 12:00:36,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ef4811b-f2d0-4f9d-a269-63f25441286e/dqc_reference
[2024-01-24 12:00:39,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,382] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg824f3daf-8b84-4c66-928d-db47d8db2461/GCF_030160835.1_ASM3016083v1_genomic.fna.gz | prodigal -d GCF_030160835.1_ASM3016083v1_genomic.fna/cds.fna -a GCF_030160835.1_ASM3016083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:01:02,511] [INFO] Task succeeded: Prodigal
[2024-01-24 12:01:02,512] [INFO] Task started: HMMsearch
[2024-01-24 12:01:02,512] [INFO] Running command: hmmsearch --tblout GCF_030160835.1_ASM3016083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ef4811b-f2d0-4f9d-a269-63f25441286e/dqc_reference/reference_markers.hmm GCF_030160835.1_ASM3016083v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:01:02,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:01:02,861] [INFO] Found 6/6 markers.
[2024-01-24 12:01:02,924] [INFO] Query marker FASTA was written to GCF_030160835.1_ASM3016083v1_genomic.fna/markers.fasta
[2024-01-24 12:01:02,925] [INFO] Task started: Blastn
[2024-01-24 12:01:02,925] [INFO] Running command: blastn -query GCF_030160835.1_ASM3016083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ef4811b-f2d0-4f9d-a269-63f25441286e/dqc_reference/reference_markers.fasta -out GCF_030160835.1_ASM3016083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:03,978] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:03,982] [INFO] Selected 31 target genomes.
[2024-01-24 12:01:03,983] [INFO] Target genome list was writen to GCF_030160835.1_ASM3016083v1_genomic.fna/target_genomes.txt
[2024-01-24 12:01:04,033] [INFO] Task started: fastANI
[2024-01-24 12:01:04,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg824f3daf-8b84-4c66-928d-db47d8db2461/GCF_030160835.1_ASM3016083v1_genomic.fna.gz --refList GCF_030160835.1_ASM3016083v1_genomic.fna/target_genomes.txt --output GCF_030160835.1_ASM3016083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:31,271] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:31,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ef4811b-f2d0-4f9d-a269-63f25441286e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:31,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ef4811b-f2d0-4f9d-a269-63f25441286e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:31,301] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:01:31,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:01:31,301] [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
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	78.0442	429	2541	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.9425	413	2541	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.9284	408	2541	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.8257	422	2541	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.6695	393	2541	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.665	449	2541	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.6348	335	2541	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	77.6122	442	2541	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.6054	333	2541	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.5899	417	2541	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	77.5114	343	2541	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.4986	324	2541	95	below_threshold
Rhabdaerophilum calidifontis	strain=SYSU G02060	GCA_008641065.1	2604328	2604328	type	True	77.4897	275	2541	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	77.4729	358	2541	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	77.4547	361	2541	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	77.4347	252	2541	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	77.3494	335	2541	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	77.3179	320	2541	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	77.2613	322	2541	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.2277	362	2541	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	77.227	417	2541	95	below_threshold
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	77.2261	418	2541	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.2052	388	2541	95	below_threshold
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	77.1903	375	2541	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	77.1877	421	2541	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.1798	402	2541	95	below_threshold
Microvirga flavescens	strain=c27j1	GCA_003290125.1	2249811	2249811	type	True	77.1195	265	2541	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	77.0699	395	2541	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.0515	418	2541	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.9167	447	2541	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.8976	304	2541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:31,303] [INFO] DFAST Taxonomy check result was written to GCF_030160835.1_ASM3016083v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:31,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:31,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:31,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ef4811b-f2d0-4f9d-a269-63f25441286e/dqc_reference/checkm_data
[2024-01-24 12:01:31,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:31,382] [INFO] Task started: CheckM
[2024-01-24 12:01:31,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160835.1_ASM3016083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160835.1_ASM3016083v1_genomic.fna/checkm_input GCF_030160835.1_ASM3016083v1_genomic.fna/checkm_result
[2024-01-24 12:02:36,447] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:36,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:36,506] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:36,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:36,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160835.1_ASM3016083v1_genomic.fna/markers.fasta)
[2024-01-24 12:02:36,508] [INFO] Task started: Blastn
[2024-01-24 12:02:36,508] [INFO] Running command: blastn -query GCF_030160835.1_ASM3016083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ef4811b-f2d0-4f9d-a269-63f25441286e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160835.1_ASM3016083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:02:38,501] [INFO] Task succeeded: Blastn
[2024-01-24 12:02:38,506] [INFO] Selected 17 target genomes.
[2024-01-24 12:02:38,506] [INFO] Target genome list was writen to GCF_030160835.1_ASM3016083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:02:38,521] [INFO] Task started: fastANI
[2024-01-24 12:02:38,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg824f3daf-8b84-4c66-928d-db47d8db2461/GCF_030160835.1_ASM3016083v1_genomic.fna.gz --refList GCF_030160835.1_ASM3016083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160835.1_ASM3016083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:56,457] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:56,485] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:02:56,485] [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_002982075.1	s__Labrys okinawensis	82.3331	1181	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	98.61	98.61	0.96	0.96	2	-
GCF_001676615.1	s__Labrys sp001676615	82.1765	1198	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008330945.1	s__Labrys sp008330945	82.1073	1226	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466745.1	s__Bosea sp900466745	77.9269	450	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_003208615.1	s__Bosea sp003208615	77.7908	452	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390635.1	s__Ancylobacter_C lacus	77.727	403	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220095.1	s__Bosea sp002220095	77.6233	418	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.6177	338	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506165.1	s__Bosea sp902506165	77.5662	489	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.97	1.00	1.00	8	-
GCF_004341515.1	s__Bosea sp004341515	77.4586	532	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849325.1	s__Xanthobacter autotrophicus_B	77.344	248	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	77.3262	344	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793505.1	s__GCA-013693735 sp016793505	77.2514	361	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	77.2409	360	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	77.2074	421	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003290125.1	s__Microvirga flavescens	77.111	266	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043895.1	s__Methylobacterium indicum	77.07	397	2541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:56,487] [INFO] GTDB search result was written to GCF_030160835.1_ASM3016083v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:56,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:56,494] [INFO] DFAST_QC result json was written to GCF_030160835.1_ASM3016083v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:56,494] [INFO] DFAST_QC completed!
[2024-01-24 12:02:56,494] [INFO] Total running time: 0h2m20s