[2024-01-24 13:01:12,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,120] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fb3c596-bc79-43d0-a723-4ee1ffc7127c/dqc_reference
[2024-01-24 13:01:13,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,455] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg453a5da0-9656-47ff-92db-8803f8e3d97b/GCF_019443285.1_ASM1944328v1_genomic.fna.gz | prodigal -d GCF_019443285.1_ASM1944328v1_genomic.fna/cds.fna -a GCF_019443285.1_ASM1944328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:24,939] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:24,939] [INFO] Task started: HMMsearch
[2024-01-24 13:01:24,939] [INFO] Running command: hmmsearch --tblout GCF_019443285.1_ASM1944328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fb3c596-bc79-43d0-a723-4ee1ffc7127c/dqc_reference/reference_markers.hmm GCF_019443285.1_ASM1944328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:25,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:25,229] [INFO] Found 6/6 markers.
[2024-01-24 13:01:25,260] [INFO] Query marker FASTA was written to GCF_019443285.1_ASM1944328v1_genomic.fna/markers.fasta
[2024-01-24 13:01:25,261] [INFO] Task started: Blastn
[2024-01-24 13:01:25,261] [INFO] Running command: blastn -query GCF_019443285.1_ASM1944328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fb3c596-bc79-43d0-a723-4ee1ffc7127c/dqc_reference/reference_markers.fasta -out GCF_019443285.1_ASM1944328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:26,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:26,193] [INFO] Selected 26 target genomes.
[2024-01-24 13:01:26,193] [INFO] Target genome list was writen to GCF_019443285.1_ASM1944328v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:26,207] [INFO] Task started: fastANI
[2024-01-24 13:01:26,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg453a5da0-9656-47ff-92db-8803f8e3d97b/GCF_019443285.1_ASM1944328v1_genomic.fna.gz --refList GCF_019443285.1_ASM1944328v1_genomic.fna/target_genomes.txt --output GCF_019443285.1_ASM1944328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:43,801] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:43,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fb3c596-bc79-43d0-a723-4ee1ffc7127c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:43,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fb3c596-bc79-43d0-a723-4ee1ffc7127c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:43,821] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:43,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:43,821] [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
Aquisediminimonas profunda	strain=DS48-3	GCA_019443285.1	1550733	1550733	type	True	100.0	1135	1135	95	conclusive
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.5508	147	1135	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	77.5173	122	1135	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	77.4649	117	1135	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	77.3788	90	1135	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.3521	183	1135	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.3337	141	1135	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	77.3246	91	1135	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.2501	152	1135	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	77.1873	128	1135	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.1697	141	1135	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	77.1285	155	1135	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	77.1236	136	1135	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	77.114	103	1135	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	77.0992	139	1135	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	77.0957	133	1135	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	77.0554	126	1135	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.0211	104	1135	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	76.9623	124	1135	95	below_threshold
Sphingomonas paeninsulae	strain=YZ-8	GCA_003660165.1	2319844	2319844	type	True	76.9284	89	1135	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.8976	145	1135	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	76.8335	141	1135	95	below_threshold
Sphingobium algorifonticola	strain=TLA-22	GCA_004005485.1	2008318	2008318	type	True	76.5801	137	1135	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	76.3051	54	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:43,823] [INFO] DFAST Taxonomy check result was written to GCF_019443285.1_ASM1944328v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:43,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:43,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:43,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fb3c596-bc79-43d0-a723-4ee1ffc7127c/dqc_reference/checkm_data
[2024-01-24 13:01:43,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:43,860] [INFO] Task started: CheckM
[2024-01-24 13:01:43,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019443285.1_ASM1944328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019443285.1_ASM1944328v1_genomic.fna/checkm_input GCF_019443285.1_ASM1944328v1_genomic.fna/checkm_result
[2024-01-24 13:02:20,183] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:20,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,205] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:20,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:20,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019443285.1_ASM1944328v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:20,206] [INFO] Task started: Blastn
[2024-01-24 13:02:20,206] [INFO] Running command: blastn -query GCF_019443285.1_ASM1944328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fb3c596-bc79-43d0-a723-4ee1ffc7127c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019443285.1_ASM1944328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:21,680] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:21,683] [INFO] Selected 26 target genomes.
[2024-01-24 13:02:21,683] [INFO] Target genome list was writen to GCF_019443285.1_ASM1944328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:21,715] [INFO] Task started: fastANI
[2024-01-24 13:02:21,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg453a5da0-9656-47ff-92db-8803f8e3d97b/GCF_019443285.1_ASM1944328v1_genomic.fna.gz --refList GCF_019443285.1_ASM1944328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019443285.1_ASM1944328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:35,308] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:35,326] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:35,326] [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_016704425.1	s__Chakrabartia sp016704425	87.1768	706	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	98.81	97.63	0.91	0.86	10	-
GCA_016714795.1	s__Chakrabartia sp016714795	77.6155	178	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	77.4928	146	1135	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_017987825.1	s__Sphingorhabdus_B sp017987825	77.4739	91	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720115.1	s__Sphingorhabdus_B sp016720115	77.4606	144	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.85	99.81	0.95	0.95	3	-
GCA_005518185.1	s__Chakrabartia godavariana	77.4354	223	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	77.314	142	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	77.3003	145	1135	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_000382885.1	s__Sphingobium japonicum_C	77.2949	115	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721875.1	s__Sphingorhabdus_B sp016721875	77.2466	100	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.47	99.39	0.95	0.94	3	-
GCF_002953135.1	s__Sphingobium sp002953135	77.2291	107	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556185.1	s__Sphingomonas sp001556185	77.2023	154	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.51	96.51	0.87	0.87	2	-
GCF_000281715.1	s__Sphingobium sp000281715	77.1186	124	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821605.1	s__UBA6174 sp903821605	77.0737	118	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA6174	95.0	99.98	99.98	0.97	0.97	2	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	77.0554	126	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	77.0444	103	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650735.1	s__Sphingomonas sp001650735	77.0377	131	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280555.1	s__Sphingomonas sp002280555	77.0331	120	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.55	97.47	0.91	0.90	3	-
GCA_903958285.1	s__Chakrabartia sp903958285	77.0118	126	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	76.912	144	1135	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_005144715.1	s__Sphingomonas sp005144715	76.8335	141	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821585.1	s__UBA1936 sp013821585	76.6	102	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA1936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478575.1	s__Chakrabartia sp002478575	76.588	83	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516475.1	s__Parasphingorhabdus sp012516475	76.3051	54	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:35,329] [INFO] GTDB search result was written to GCF_019443285.1_ASM1944328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:35,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:35,334] [INFO] DFAST_QC result json was written to GCF_019443285.1_ASM1944328v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:35,334] [INFO] DFAST_QC completed!
[2024-01-24 13:02:35,334] [INFO] Total running time: 0h1m23s