[2024-01-24 14:05:34,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b2fd9dd-c290-4029-b652-7352cd0c4ba1/dqc_reference
[2024-01-24 14:05:35,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,540] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a22273b-69f8-4a8c-8198-9ef57b1aa115/GCF_014200045.1_ASM1420004v1_genomic.fna.gz | prodigal -d GCF_014200045.1_ASM1420004v1_genomic.fna/cds.fna -a GCF_014200045.1_ASM1420004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:46,529] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:46,529] [INFO] Task started: HMMsearch
[2024-01-24 14:05:46,529] [INFO] Running command: hmmsearch --tblout GCF_014200045.1_ASM1420004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b2fd9dd-c290-4029-b652-7352cd0c4ba1/dqc_reference/reference_markers.hmm GCF_014200045.1_ASM1420004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:46,756] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:46,757] [INFO] Found 6/6 markers.
[2024-01-24 14:05:46,792] [INFO] Query marker FASTA was written to GCF_014200045.1_ASM1420004v1_genomic.fna/markers.fasta
[2024-01-24 14:05:46,792] [INFO] Task started: Blastn
[2024-01-24 14:05:46,793] [INFO] Running command: blastn -query GCF_014200045.1_ASM1420004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b2fd9dd-c290-4029-b652-7352cd0c4ba1/dqc_reference/reference_markers.fasta -out GCF_014200045.1_ASM1420004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:47,606] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:47,609] [INFO] Selected 28 target genomes.
[2024-01-24 14:05:47,610] [INFO] Target genome list was writen to GCF_014200045.1_ASM1420004v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:47,626] [INFO] Task started: fastANI
[2024-01-24 14:05:47,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a22273b-69f8-4a8c-8198-9ef57b1aa115/GCF_014200045.1_ASM1420004v1_genomic.fna.gz --refList GCF_014200045.1_ASM1420004v1_genomic.fna/target_genomes.txt --output GCF_014200045.1_ASM1420004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,763] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b2fd9dd-c290-4029-b652-7352cd0c4ba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b2fd9dd-c290-4029-b652-7352cd0c4ba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,785] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:07,785] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:07,785] [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
Rhizorhapis suberifaciens	strain=DSM 7465	GCA_014200045.1	13656	13656	type	True	100.0	1102	1102	95	conclusive
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	77.9925	252	1102	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	77.9483	266	1102	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	77.928	267	1102	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	77.9232	255	1102	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	77.9182	266	1102	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	77.8966	260	1102	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	77.8835	259	1102	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	77.8679	266	1102	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	77.8213	263	1102	95	below_threshold
Sphingobium subterraneum	strain=DSM 102255	GCA_014199435.1	627688	627688	type	True	77.7376	194	1102	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.7241	181	1102	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	77.6541	267	1102	95	below_threshold
Sphingobium bisphenolivorans	strain=YL23	GCA_000412635.1	1335760	1335760	type	True	77.6148	243	1102	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	77.5985	246	1102	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	77.5755	96	1102	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	77.4536	243	1102	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.3149	212	1102	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.2443	164	1102	95	below_threshold
Aurantiacibacter atlanticus	strain=s21-N3	GCA_001077815.2	1648404	1648404	type	True	77.2412	69	1102	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	77.2275	167	1102	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.2059	67	1102	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.1283	113	1102	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.906	150	1102	95	below_threshold
Alteripontixanthobacter maritimus	strain=HME9302	GCA_003340475.1	2161824	2161824	type	True	76.8172	69	1102	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	76.8078	107	1102	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	76.7313	116	1102	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	76.6059	154	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,787] [INFO] DFAST Taxonomy check result was written to GCF_014200045.1_ASM1420004v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,788] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b2fd9dd-c290-4029-b652-7352cd0c4ba1/dqc_reference/checkm_data
[2024-01-24 14:06:07,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,826] [INFO] Task started: CheckM
[2024-01-24 14:06:07,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014200045.1_ASM1420004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014200045.1_ASM1420004v1_genomic.fna/checkm_input GCF_014200045.1_ASM1420004v1_genomic.fna/checkm_result
[2024-01-24 14:06:41,911] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:41,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:41,927] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:41,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:41,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014200045.1_ASM1420004v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:41,928] [INFO] Task started: Blastn
[2024-01-24 14:06:41,928] [INFO] Running command: blastn -query GCF_014200045.1_ASM1420004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b2fd9dd-c290-4029-b652-7352cd0c4ba1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014200045.1_ASM1420004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:43,291] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:43,294] [INFO] Selected 26 target genomes.
[2024-01-24 14:06:43,294] [INFO] Target genome list was writen to GCF_014200045.1_ASM1420004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:43,372] [INFO] Task started: fastANI
[2024-01-24 14:06:43,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a22273b-69f8-4a8c-8198-9ef57b1aa115/GCF_014200045.1_ASM1420004v1_genomic.fna.gz --refList GCF_014200045.1_ASM1420004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014200045.1_ASM1420004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:01,433] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:01,455] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:01,456] [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_014200045.1	s__Rhizorhapis suberifaciens	100.0	1102	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhapis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016650315.1	s__Rhizorhapis sp016650315	78.518	232	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhapis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	78.1281	259	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001456115.1	s__Sphingobium baderi_A	78.0368	268	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	78.0115	250	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
GCF_001005725.1	s__Sphingobium chungbukense	77.8966	260	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_007830065.1	s__Sphingobium wenxiniae	77.8679	266	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	-
GCF_004361945.1	s__Sphingobium barthaii_A	77.8443	264	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590775.1	s__Sphingobium_A sp003590775	77.7416	180	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	77.7241	233	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199435.1	s__Sphingobium subterraneum	77.7201	195	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000588875.1	s__Sphingobium sp000588875	77.6992	241	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	77.6709	242	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196495.1	s__Sphingobium jiangsuense	77.6541	267	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	77.6038	256	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196635.1	s__Sphingobium fontiphilum	77.602	247	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412635.1	s__Sphingobium bisphenolivorans	77.6003	244	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	77.4419	137	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911745.1	s__Sphingobium sp013911745	77.4133	200	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	77.3888	89	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278035.1	s__Sphingopyxis sp001278035	77.315	129	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	77.2729	151	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_003171655.1	s__Sphingomonas portus	77.2253	167	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	77.2057	200	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	76.6199	153	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823985.1	s__Sphingorhabdus_B sp013823985	76.3788	90	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,459] [INFO] GTDB search result was written to GCF_014200045.1_ASM1420004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:01,460] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:01,465] [INFO] DFAST_QC result json was written to GCF_014200045.1_ASM1420004v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:01,466] [INFO] DFAST_QC completed!
[2024-01-24 14:07:01,466] [INFO] Total running time: 0h1m27s