[2024-01-24 11:59:11,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:11,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:11,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d2d4cc8-c178-4722-a8ea-6d0827445365/dqc_reference
[2024-01-24 11:59:13,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:13,028] [INFO] Task started: Prodigal
[2024-01-24 11:59:13,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg081f5075-5abd-4b36-9493-3fb7bcc808f6/GCF_011762045.1_ASM1176204v1_genomic.fna.gz | prodigal -d GCF_011762045.1_ASM1176204v1_genomic.fna/cds.fna -a GCF_011762045.1_ASM1176204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:27,747] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:27,747] [INFO] Task started: HMMsearch
[2024-01-24 11:59:27,747] [INFO] Running command: hmmsearch --tblout GCF_011762045.1_ASM1176204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d2d4cc8-c178-4722-a8ea-6d0827445365/dqc_reference/reference_markers.hmm GCF_011762045.1_ASM1176204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:28,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:28,071] [INFO] Found 6/6 markers.
[2024-01-24 11:59:28,113] [INFO] Query marker FASTA was written to GCF_011762045.1_ASM1176204v1_genomic.fna/markers.fasta
[2024-01-24 11:59:28,114] [INFO] Task started: Blastn
[2024-01-24 11:59:28,114] [INFO] Running command: blastn -query GCF_011762045.1_ASM1176204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2d4cc8-c178-4722-a8ea-6d0827445365/dqc_reference/reference_markers.fasta -out GCF_011762045.1_ASM1176204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:29,107] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:29,110] [INFO] Selected 26 target genomes.
[2024-01-24 11:59:29,111] [INFO] Target genome list was writen to GCF_011762045.1_ASM1176204v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:29,120] [INFO] Task started: fastANI
[2024-01-24 11:59:29,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg081f5075-5abd-4b36-9493-3fb7bcc808f6/GCF_011762045.1_ASM1176204v1_genomic.fna.gz --refList GCF_011762045.1_ASM1176204v1_genomic.fna/target_genomes.txt --output GCF_011762045.1_ASM1176204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:56,182] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:56,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d2d4cc8-c178-4722-a8ea-6d0827445365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:56,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d2d4cc8-c178-4722-a8ea-6d0827445365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:56,205] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:56,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:56,205] [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
Rhizomicrobium electricum	strain=DSM 21034	GCA_011762045.1	480070	480070	type	True	100.0	1568	1570	95	conclusive
Rhizomicrobium palustre	strain=DSM 19867	GCA_011761565.1	189966	189966	type	True	79.2805	602	1570	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.2479	189	1570	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.8571	216	1570	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.8141	126	1570	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	76.7652	235	1570	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	76.7505	133	1570	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.7468	176	1570	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	76.7183	151	1570	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	76.6981	148	1570	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	76.6957	232	1570	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.6415	168	1570	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	76.6359	156	1570	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	76.6287	185	1570	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	76.6285	218	1570	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	76.6267	185	1570	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.6152	201	1570	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.6097	191	1570	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.5877	179	1570	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.4996	177	1570	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.4174	151	1570	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.3929	207	1570	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.1738	182	1570	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.0345	165	1570	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.0339	216	1570	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9265	208	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:56,207] [INFO] DFAST Taxonomy check result was written to GCF_011762045.1_ASM1176204v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:56,209] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:56,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:56,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d2d4cc8-c178-4722-a8ea-6d0827445365/dqc_reference/checkm_data
[2024-01-24 11:59:56,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:56,273] [INFO] Task started: CheckM
[2024-01-24 11:59:56,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011762045.1_ASM1176204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011762045.1_ASM1176204v1_genomic.fna/checkm_input GCF_011762045.1_ASM1176204v1_genomic.fna/checkm_result
[2024-01-24 12:00:40,827] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:40,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:40,852] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:40,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:40,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011762045.1_ASM1176204v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:40,853] [INFO] Task started: Blastn
[2024-01-24 12:00:40,853] [INFO] Running command: blastn -query GCF_011762045.1_ASM1176204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2d4cc8-c178-4722-a8ea-6d0827445365/dqc_reference/reference_markers_gtdb.fasta -out GCF_011762045.1_ASM1176204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:42,651] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:42,654] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:42,655] [INFO] Target genome list was writen to GCF_011762045.1_ASM1176204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:42,662] [INFO] Task started: fastANI
[2024-01-24 12:00:42,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg081f5075-5abd-4b36-9493-3fb7bcc808f6/GCF_011762045.1_ASM1176204v1_genomic.fna.gz --refList GCF_011762045.1_ASM1176204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011762045.1_ASM1176204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:50,673] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:50,692] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:50,692] [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_011762045.1	s__Rhizomicrobium electricum	100.0	1568	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002307725.1	s__Rhizomicrobium sp002307725	81.9361	824	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654715.1	s__Rhizomicrobium sp015654715	81.6302	518	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149165.1	s__Rhizomicrobium sp013149165	79.9129	716	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761565.1	s__Rhizomicrobium palustre	79.2879	601	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158585.1	s__Rhizomicrobium sp003158585	78.7199	503	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654635.1	s__Rhizomicrobium sp015654635	78.6249	497	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970685.1	s__Rhizomicrobium sp018970685	77.9728	268	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245415.1	s__Rhizomicrobium sp019245415	77.9616	324	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	99.94	99.94	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:50,694] [INFO] GTDB search result was written to GCF_011762045.1_ASM1176204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:50,695] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:50,701] [INFO] DFAST_QC result json was written to GCF_011762045.1_ASM1176204v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:50,701] [INFO] DFAST_QC completed!
[2024-01-24 12:00:50,701] [INFO] Total running time: 0h1m39s