[2024-01-24 12:53:55,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:55,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:55,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg69ecb717-2c50-47a1-bb99-44e00f1ad0a8/dqc_reference
[2024-01-24 12:53:56,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:56,291] [INFO] Task started: Prodigal
[2024-01-24 12:53:56,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bcdfc14-eb3c-4bca-af1c-af4903b8acf8/GCF_001890385.1_ASM189038v1_genomic.fna.gz | prodigal -d GCF_001890385.1_ASM189038v1_genomic.fna/cds.fna -a GCF_001890385.1_ASM189038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:07,941] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:07,942] [INFO] Task started: HMMsearch
[2024-01-24 12:54:07,942] [INFO] Running command: hmmsearch --tblout GCF_001890385.1_ASM189038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69ecb717-2c50-47a1-bb99-44e00f1ad0a8/dqc_reference/reference_markers.hmm GCF_001890385.1_ASM189038v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:08,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:08,253] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5bcdfc14-eb3c-4bca-af1c-af4903b8acf8/GCF_001890385.1_ASM189038v1_genomic.fna.gz]
[2024-01-24 12:54:08,295] [INFO] Query marker FASTA was written to GCF_001890385.1_ASM189038v1_genomic.fna/markers.fasta
[2024-01-24 12:54:08,295] [INFO] Task started: Blastn
[2024-01-24 12:54:08,296] [INFO] Running command: blastn -query GCF_001890385.1_ASM189038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69ecb717-2c50-47a1-bb99-44e00f1ad0a8/dqc_reference/reference_markers.fasta -out GCF_001890385.1_ASM189038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:09,143] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:09,146] [INFO] Selected 24 target genomes.
[2024-01-24 12:54:09,147] [INFO] Target genome list was writen to GCF_001890385.1_ASM189038v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:09,158] [INFO] Task started: fastANI
[2024-01-24 12:54:09,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcdfc14-eb3c-4bca-af1c-af4903b8acf8/GCF_001890385.1_ASM189038v1_genomic.fna.gz --refList GCF_001890385.1_ASM189038v1_genomic.fna/target_genomes.txt --output GCF_001890385.1_ASM189038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:27,086] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:27,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69ecb717-2c50-47a1-bb99-44e00f1ad0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:27,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69ecb717-2c50-47a1-bb99-44e00f1ad0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:27,106] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:27,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:27,107] [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
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	100.0	1258	1261	95	conclusive
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	79.9373	292	1261	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	79.2218	229	1261	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.9689	323	1261	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	78.7363	221	1261	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	78.5918	241	1261	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	78.3452	187	1261	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.3262	261	1261	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.1797	281	1261	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	78.1226	241	1261	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.0988	262	1261	95	below_threshold
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	77.9027	199	1261	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	77.8985	210	1261	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.8623	234	1261	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.8514	202	1261	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	77.7141	185	1261	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	77.569	176	1261	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	77.5441	209	1261	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	77.5099	149	1261	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.4647	236	1261	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	77.4334	140	1261	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	77.4165	162	1261	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	77.3585	163	1261	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	76.7847	139	1261	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:27,110] [INFO] DFAST Taxonomy check result was written to GCF_001890385.1_ASM189038v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:27,114] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:27,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:27,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69ecb717-2c50-47a1-bb99-44e00f1ad0a8/dqc_reference/checkm_data
[2024-01-24 12:54:27,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:27,176] [INFO] Task started: CheckM
[2024-01-24 12:54:27,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001890385.1_ASM189038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001890385.1_ASM189038v1_genomic.fna/checkm_input GCF_001890385.1_ASM189038v1_genomic.fna/checkm_result
[2024-01-24 12:55:03,006] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:03,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:03,027] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:03,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:03,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001890385.1_ASM189038v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:03,028] [INFO] Task started: Blastn
[2024-01-24 12:55:03,028] [INFO] Running command: blastn -query GCF_001890385.1_ASM189038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69ecb717-2c50-47a1-bb99-44e00f1ad0a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001890385.1_ASM189038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:04,435] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:04,441] [INFO] Selected 23 target genomes.
[2024-01-24 12:55:04,441] [INFO] Target genome list was writen to GCF_001890385.1_ASM189038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:04,456] [INFO] Task started: fastANI
[2024-01-24 12:55:04,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcdfc14-eb3c-4bca-af1c-af4903b8acf8/GCF_001890385.1_ASM189038v1_genomic.fna.gz --refList GCF_001890385.1_ASM189038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001890385.1_ASM189038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:19,349] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:19,367] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:19,367] [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_001890385.1	s__Tardibacter chloracetimidivorans	100.0	1257	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tardibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167915.1	s__Rhizorhabdus histidinilytica	79.2475	303	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_000739895.2	s__Sphingomonas paucimobilis	79.2065	229	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
GCF_003034225.1	s__Sphingomonas_E fennica	78.9421	325	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.9253	317	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	78.6723	341	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_003129465.1	s__Allosphingosinicella humi	78.3659	186	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	78.3259	261	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	78.308	249	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785815.1	s__Sphingomonas_G solaris	78.1079	242	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.1075	202	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	78.104	281	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	77.8861	210	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634215.1	s__Sphingosinicella microcystinivorans	77.8859	200	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_014230305.1	s__Novosphingobium aerophilum	77.7349	183	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	77.5464	162	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	77.514	176	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_903643065.1	s__Sphingomonas sp903643065	77.5036	134	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590965.1	s__Novosphingobium lentum	77.5007	212	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097155.1	s__Glacieibacterium frigidum	77.4863	171	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	77.4647	236	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720465.1	s__Erythrobacter sp001720465	77.4262	138	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205635.1	s__Polymorphobacter multimanifer	77.4165	162	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.78	99.78	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:19,369] [INFO] GTDB search result was written to GCF_001890385.1_ASM189038v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:19,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:19,374] [INFO] DFAST_QC result json was written to GCF_001890385.1_ASM189038v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:19,374] [INFO] DFAST_QC completed!
[2024-01-24 12:55:19,374] [INFO] Total running time: 0h1m24s