[2024-01-25 18:02:35,565] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:35,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:35,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg442544f4-3d71-4d02-8664-7a2095caaaec/dqc_reference
[2024-01-25 18:02:36,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:36,769] [INFO] Task started: Prodigal
[2024-01-25 18:02:36,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg95840639-3cd0-41bf-ab5f-fe3d9fb0d554/GCF_014199215.1_ASM1419921v1_genomic.fna.gz | prodigal -d GCF_014199215.1_ASM1419921v1_genomic.fna/cds.fna -a GCF_014199215.1_ASM1419921v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:47,863] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:47,863] [INFO] Task started: HMMsearch
[2024-01-25 18:02:47,863] [INFO] Running command: hmmsearch --tblout GCF_014199215.1_ASM1419921v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg442544f4-3d71-4d02-8664-7a2095caaaec/dqc_reference/reference_markers.hmm GCF_014199215.1_ASM1419921v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:48,098] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:48,099] [INFO] Found 6/6 markers.
[2024-01-25 18:02:48,136] [INFO] Query marker FASTA was written to GCF_014199215.1_ASM1419921v1_genomic.fna/markers.fasta
[2024-01-25 18:02:48,136] [INFO] Task started: Blastn
[2024-01-25 18:02:48,136] [INFO] Running command: blastn -query GCF_014199215.1_ASM1419921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg442544f4-3d71-4d02-8664-7a2095caaaec/dqc_reference/reference_markers.fasta -out GCF_014199215.1_ASM1419921v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:49,002] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:49,004] [INFO] Selected 20 target genomes.
[2024-01-25 18:02:49,005] [INFO] Target genome list was writen to GCF_014199215.1_ASM1419921v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:49,026] [INFO] Task started: fastANI
[2024-01-25 18:02:49,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg95840639-3cd0-41bf-ab5f-fe3d9fb0d554/GCF_014199215.1_ASM1419921v1_genomic.fna.gz --refList GCF_014199215.1_ASM1419921v1_genomic.fna/target_genomes.txt --output GCF_014199215.1_ASM1419921v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:05,445] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:05,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg442544f4-3d71-4d02-8664-7a2095caaaec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:05,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg442544f4-3d71-4d02-8664-7a2095caaaec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:05,458] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:05,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:05,458] [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
Sphingobium boeckii	strain=DSM 25079	GCA_014199215.1	1082345	1082345	type	True	100.0	1336	1337	95	conclusive
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	79.4652	600	1337	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.9178	540	1337	95	below_threshold
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	78.2984	360	1337	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.1265	369	1337	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.1026	369	1337	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.0815	356	1337	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	78.0388	401	1337	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	77.9699	340	1337	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	77.9693	351	1337	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	77.9581	344	1337	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.9451	366	1337	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	77.9307	337	1337	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	77.8697	344	1337	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.8295	366	1337	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	77.709	331	1337	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.6006	309	1337	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	77.518	318	1337	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.3003	278	1337	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.2124	237	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:05,463] [INFO] DFAST Taxonomy check result was written to GCF_014199215.1_ASM1419921v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:05,467] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:05,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:05,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg442544f4-3d71-4d02-8664-7a2095caaaec/dqc_reference/checkm_data
[2024-01-25 18:03:05,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:05,516] [INFO] Task started: CheckM
[2024-01-25 18:03:05,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199215.1_ASM1419921v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199215.1_ASM1419921v1_genomic.fna/checkm_input GCF_014199215.1_ASM1419921v1_genomic.fna/checkm_result
[2024-01-25 18:03:43,218] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:43,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:43,256] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:43,256] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:43,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199215.1_ASM1419921v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:43,257] [INFO] Task started: Blastn
[2024-01-25 18:03:43,257] [INFO] Running command: blastn -query GCF_014199215.1_ASM1419921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg442544f4-3d71-4d02-8664-7a2095caaaec/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199215.1_ASM1419921v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:44,756] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:44,760] [INFO] Selected 24 target genomes.
[2024-01-25 18:03:44,760] [INFO] Target genome list was writen to GCF_014199215.1_ASM1419921v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:44,777] [INFO] Task started: fastANI
[2024-01-25 18:03:44,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg95840639-3cd0-41bf-ab5f-fe3d9fb0d554/GCF_014199215.1_ASM1419921v1_genomic.fna.gz --refList GCF_014199215.1_ASM1419921v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199215.1_ASM1419921v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:02,546] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:02,560] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:02,561] [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_014199215.1	s__Sphingobium_A boeckii	100.0	1336	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003590775.1	s__Sphingobium_A sp003590775	78.9025	543	1337	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_003240855.1	s__Sphingomonas_L sanxanigenens_A	78.3677	349	1337	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_003034225.1	s__Sphingomonas_E fennica	78.3604	409	1337	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_001423845.1	s__Sphingomonas sp001423845	78.3448	375	1337	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	78.3428	416	1337	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	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	78.2587	280	1337	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_014490665.1	s__Sphingomonas alpina	78.1732	368	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	78.1138	368	1337	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_013374115.1	s__Sphingomonas sp013374115	78.1072	280	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.0896	423	1337	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_011057975.1	s__Sphingomonas sp011057975	78.0815	356	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000803065.1	s__Sphingomonas sp000803065	78.0387	384	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197035.1	s__Sphingobium scionense	78.0304	402	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	77.9592	352	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_007785815.1	s__Sphingomonas_G solaris	77.9367	337	1337	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	77.9259	304	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	77.8287	237	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	77.6029	221	1337	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_004796535.1	s__Sphingomonas_L sp004796535	77.5779	312	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821585.1	s__UBA1936 sp013821585	77.3746	194	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA1936	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	77.3017	279	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	77.2124	237	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440635.1	s__Novosphingobium sp002440635	76.9097	207	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:02,562] [INFO] GTDB search result was written to GCF_014199215.1_ASM1419921v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:02,562] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:02,566] [INFO] DFAST_QC result json was written to GCF_014199215.1_ASM1419921v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:02,566] [INFO] DFAST_QC completed!
[2024-01-25 18:04:02,566] [INFO] Total running time: 0h1m27s