[2024-01-24 13:36:45,755] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg61a4ffeb-dce8-440d-a2a8-01ed2be88cfb/dqc_reference
[2024-01-24 13:36:47,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,099] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg27c5c3b7-7efc-418e-a8df-7c0167b8b006/GCF_022014495.1_ASM2201449v1_genomic.fna.gz | prodigal -d GCF_022014495.1_ASM2201449v1_genomic.fna/cds.fna -a GCF_022014495.1_ASM2201449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:58,110] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:58,111] [INFO] Task started: HMMsearch
[2024-01-24 13:36:58,111] [INFO] Running command: hmmsearch --tblout GCF_022014495.1_ASM2201449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61a4ffeb-dce8-440d-a2a8-01ed2be88cfb/dqc_reference/reference_markers.hmm GCF_022014495.1_ASM2201449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:58,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:58,346] [INFO] Found 6/6 markers.
[2024-01-24 13:36:58,391] [INFO] Query marker FASTA was written to GCF_022014495.1_ASM2201449v1_genomic.fna/markers.fasta
[2024-01-24 13:36:58,392] [INFO] Task started: Blastn
[2024-01-24 13:36:58,392] [INFO] Running command: blastn -query GCF_022014495.1_ASM2201449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61a4ffeb-dce8-440d-a2a8-01ed2be88cfb/dqc_reference/reference_markers.fasta -out GCF_022014495.1_ASM2201449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:59,314] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:59,317] [INFO] Selected 30 target genomes.
[2024-01-24 13:36:59,318] [INFO] Target genome list was writen to GCF_022014495.1_ASM2201449v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:59,340] [INFO] Task started: fastANI
[2024-01-24 13:36:59,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c5c3b7-7efc-418e-a8df-7c0167b8b006/GCF_022014495.1_ASM2201449v1_genomic.fna.gz --refList GCF_022014495.1_ASM2201449v1_genomic.fna/target_genomes.txt --output GCF_022014495.1_ASM2201449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:19,734] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:19,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61a4ffeb-dce8-440d-a2a8-01ed2be88cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:19,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61a4ffeb-dce8-440d-a2a8-01ed2be88cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:19,757] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:19,757] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:19,757] [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
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	78.1087	256	1254	95	below_threshold
Thermaurantiacus tibetensis	strain=SYSU G02173	GCA_015354055.1	2759035	2759035	type	True	77.867	312	1254	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.857	312	1254	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	77.8305	210	1254	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.8123	351	1254	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.8005	351	1254	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	77.7906	284	1254	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.7897	301	1254	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.701	332	1254	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	77.671	274	1254	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	77.6382	242	1254	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	77.6341	275	1254	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	77.5524	312	1254	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.5444	260	1254	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	77.5172	267	1254	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	77.4861	238	1254	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	77.4699	353	1254	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.4694	327	1254	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	77.4631	148	1254	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	77.4469	295	1254	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	77.4452	290	1254	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	77.4346	264	1254	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.2293	273	1254	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.1893	265	1254	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	77.1529	232	1254	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	77.0731	171	1254	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.062	287	1254	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	76.1482	169	1254	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	76.0702	180	1254	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	76.0526	167	1254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:19,759] [INFO] DFAST Taxonomy check result was written to GCF_022014495.1_ASM2201449v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:19,760] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:19,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:19,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61a4ffeb-dce8-440d-a2a8-01ed2be88cfb/dqc_reference/checkm_data
[2024-01-24 13:37:19,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:19,801] [INFO] Task started: CheckM
[2024-01-24 13:37:19,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022014495.1_ASM2201449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022014495.1_ASM2201449v1_genomic.fna/checkm_input GCF_022014495.1_ASM2201449v1_genomic.fna/checkm_result
[2024-01-24 13:37:57,168] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:57,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:57,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:57,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:57,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022014495.1_ASM2201449v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:57,192] [INFO] Task started: Blastn
[2024-01-24 13:37:57,192] [INFO] Running command: blastn -query GCF_022014495.1_ASM2201449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61a4ffeb-dce8-440d-a2a8-01ed2be88cfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_022014495.1_ASM2201449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:58,920] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:58,923] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:58,923] [INFO] Target genome list was writen to GCF_022014495.1_ASM2201449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:58,953] [INFO] Task started: fastANI
[2024-01-24 13:37:58,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c5c3b7-7efc-418e-a8df-7c0167b8b006/GCF_022014495.1_ASM2201449v1_genomic.fna.gz --refList GCF_022014495.1_ASM2201449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022014495.1_ASM2201449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:11,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:11,414] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:11,415] [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
GCA_003248865.1	s__Sandaracinobacter sp003248865	81.939	613	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385875.1	s__Sandaracinobacter neustonicus	81.4985	620	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464365.1	s__Sandaracinobacter sp016464365	80.8646	585	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422985.1	s__Sandaracinobacter sp002422985	78.6889	314	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117445.1	s__GCA-014117445 sp014117445	78.5168	377	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__GCA-014117445	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	77.7611	305	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	77.6817	334	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	77.5342	236	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_003345355.1	s__Sphingomonas sp003345355	77.534	261	1254	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	77.4186	281	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355005.1	s__Sphingomonas sp003355005	77.4169	247	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	77.3634	243	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	77.1824	294	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	76.0741	181	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:11,418] [INFO] GTDB search result was written to GCF_022014495.1_ASM2201449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:11,419] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:11,424] [INFO] DFAST_QC result json was written to GCF_022014495.1_ASM2201449v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:11,425] [INFO] DFAST_QC completed!
[2024-01-24 13:38:11,425] [INFO] Total running time: 0h1m26s