[2024-01-25 18:48:05,572] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:05,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:05,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7855216-74b0-4c22-b73f-0f143b68837c/dqc_reference
[2024-01-25 18:48:06,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:06,730] [INFO] Task started: Prodigal
[2024-01-25 18:48:06,730] [INFO] Running command: gunzip -c /var/lib/cwl/stg04247347-d33a-4977-b10b-6ba294c1fd3b/GCF_015354055.1_ASM1535405v1_genomic.fna.gz | prodigal -d GCF_015354055.1_ASM1535405v1_genomic.fna/cds.fna -a GCF_015354055.1_ASM1535405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:13,582] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:13,583] [INFO] Task started: HMMsearch
[2024-01-25 18:48:13,583] [INFO] Running command: hmmsearch --tblout GCF_015354055.1_ASM1535405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7855216-74b0-4c22-b73f-0f143b68837c/dqc_reference/reference_markers.hmm GCF_015354055.1_ASM1535405v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:13,789] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:13,790] [INFO] Found 6/6 markers.
[2024-01-25 18:48:13,814] [INFO] Query marker FASTA was written to GCF_015354055.1_ASM1535405v1_genomic.fna/markers.fasta
[2024-01-25 18:48:13,814] [INFO] Task started: Blastn
[2024-01-25 18:48:13,814] [INFO] Running command: blastn -query GCF_015354055.1_ASM1535405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7855216-74b0-4c22-b73f-0f143b68837c/dqc_reference/reference_markers.fasta -out GCF_015354055.1_ASM1535405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:14,643] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:14,646] [INFO] Selected 25 target genomes.
[2024-01-25 18:48:14,647] [INFO] Target genome list was writen to GCF_015354055.1_ASM1535405v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:14,672] [INFO] Task started: fastANI
[2024-01-25 18:48:14,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg04247347-d33a-4977-b10b-6ba294c1fd3b/GCF_015354055.1_ASM1535405v1_genomic.fna.gz --refList GCF_015354055.1_ASM1535405v1_genomic.fna/target_genomes.txt --output GCF_015354055.1_ASM1535405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:31,739] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:31,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7855216-74b0-4c22-b73f-0f143b68837c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:31,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7855216-74b0-4c22-b73f-0f143b68837c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:31,753] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:48:31,753] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:31,754] [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
Thermaurantiacus tibetensis	strain=SYSU G02173	GCA_015354055.1	2759035	2759035	type	True	100.0	907	909	95	conclusive
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	77.095	178	909	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.0369	217	909	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	76.9967	138	909	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	76.9783	139	909	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	76.9782	198	909	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	76.9401	202	909	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	76.9145	215	909	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.8984	185	909	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	76.8242	191	909	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.8032	226	909	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	76.7684	178	909	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	76.7126	251	909	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.6739	239	909	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	76.6593	238	909	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	76.6259	219	909	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	76.5807	217	909	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	76.4973	152	909	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	76.4965	246	909	95	below_threshold
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	76.2227	105	909	95	below_threshold
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	76.2101	108	909	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	75.9843	148	909	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8056	270	909	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	75.7974	257	909	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.7677	187	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:31,755] [INFO] DFAST Taxonomy check result was written to GCF_015354055.1_ASM1535405v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:31,757] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:31,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:31,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7855216-74b0-4c22-b73f-0f143b68837c/dqc_reference/checkm_data
[2024-01-25 18:48:31,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:31,786] [INFO] Task started: CheckM
[2024-01-25 18:48:31,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015354055.1_ASM1535405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015354055.1_ASM1535405v1_genomic.fna/checkm_input GCF_015354055.1_ASM1535405v1_genomic.fna/checkm_result
[2024-01-25 18:49:10,048] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:10,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:10,069] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:10,069] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:10,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015354055.1_ASM1535405v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:10,070] [INFO] Task started: Blastn
[2024-01-25 18:49:10,070] [INFO] Running command: blastn -query GCF_015354055.1_ASM1535405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7855216-74b0-4c22-b73f-0f143b68837c/dqc_reference/reference_markers_gtdb.fasta -out GCF_015354055.1_ASM1535405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:11,609] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:11,612] [INFO] Selected 27 target genomes.
[2024-01-25 18:49:11,613] [INFO] Target genome list was writen to GCF_015354055.1_ASM1535405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:11,640] [INFO] Task started: fastANI
[2024-01-25 18:49:11,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg04247347-d33a-4977-b10b-6ba294c1fd3b/GCF_015354055.1_ASM1535405v1_genomic.fna.gz --refList GCF_015354055.1_ASM1535405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015354055.1_ASM1535405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:30,020] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:30,035] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:30,036] [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_015354055.1	s__Thermaurantiacus tibetensis	100.0	907	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Thermaurantiacus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_019245455.1	s__CAHJWT01 sp019245455	77.408	211	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248865.1	s__Sandaracinobacter sp003248865	77.1794	248	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903643075.1	s__CAHJWT01 sp903643075	77.1622	193	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994245.1	s__Sandarakinorhabdus rubra	77.1248	176	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	77.0478	216	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	77.0342	215	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117445.1	s__GCA-014117445 sp014117445	77.022	268	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__GCA-014117445	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	77.015	233	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCF_004341505.2	s__Sphingomonas sp004341505	77.007	195	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_004564275.1	s__Allosphingosinicella parva	76.9546	239	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	76.9418	201	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	76.9142	208	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097155.1	s__Glacieibacterium frigidum	76.8689	261	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018982925.1	s__Glacieibacterium sp018982925	76.7955	237	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044255.1	s__Rhizorhabdus sp011044255	76.7688	179	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793845.1	s__Sphingosinicella sp016793845	76.7047	168	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	76.6785	236	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	76.6754	236	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	76.6487	252	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	76.4272	232	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422985.1	s__Sandaracinobacter sp002422985	76.3179	141	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	76.1787	112	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	76.1632	209	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108245.1	s__Bosea lathyri	76.0812	111	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	75.7812	185	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861645.1	s__28-YEA-48 sp903861645	75.6523	100	909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	99.51	98.79	0.96	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:30,037] [INFO] GTDB search result was written to GCF_015354055.1_ASM1535405v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:30,038] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:30,041] [INFO] DFAST_QC result json was written to GCF_015354055.1_ASM1535405v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:30,042] [INFO] DFAST_QC completed!
[2024-01-25 18:49:30,042] [INFO] Total running time: 0h1m24s