[2023-06-29 20:14:08,974] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:14:08,979] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:14:08,980] [INFO] DQC Reference Directory: /var/lib/cwl/stgea4a6d54-52b5-4893-b5f6-93917ac88ff2/dqc_reference
[2023-06-29 20:14:10,444] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:14:10,445] [INFO] Task started: Prodigal
[2023-06-29 20:14:10,446] [INFO] Running command: gunzip -c /var/lib/cwl/stg5171c7a7-faab-496c-a1ed-0d586f1d854d/GCA_021732885.1_ASM2173288v1_genomic.fna.gz | prodigal -d GCA_021732885.1_ASM2173288v1_genomic.fna/cds.fna -a GCA_021732885.1_ASM2173288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:14:20,174] [INFO] Task succeeded: Prodigal
[2023-06-29 20:14:20,175] [INFO] Task started: HMMsearch
[2023-06-29 20:14:20,175] [INFO] Running command: hmmsearch --tblout GCA_021732885.1_ASM2173288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea4a6d54-52b5-4893-b5f6-93917ac88ff2/dqc_reference/reference_markers.hmm GCA_021732885.1_ASM2173288v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:14:20,458] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:14:20,459] [INFO] Found 6/6 markers.
[2023-06-29 20:14:20,503] [INFO] Query marker FASTA was written to GCA_021732885.1_ASM2173288v1_genomic.fna/markers.fasta
[2023-06-29 20:14:20,504] [INFO] Task started: Blastn
[2023-06-29 20:14:20,504] [INFO] Running command: blastn -query GCA_021732885.1_ASM2173288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea4a6d54-52b5-4893-b5f6-93917ac88ff2/dqc_reference/reference_markers.fasta -out GCA_021732885.1_ASM2173288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:21,266] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:21,270] [INFO] Selected 29 target genomes.
[2023-06-29 20:14:21,271] [INFO] Target genome list was writen to GCA_021732885.1_ASM2173288v1_genomic.fna/target_genomes.txt
[2023-06-29 20:14:21,277] [INFO] Task started: fastANI
[2023-06-29 20:14:21,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg5171c7a7-faab-496c-a1ed-0d586f1d854d/GCA_021732885.1_ASM2173288v1_genomic.fna.gz --refList GCA_021732885.1_ASM2173288v1_genomic.fna/target_genomes.txt --output GCA_021732885.1_ASM2173288v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:14:44,094] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:44,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea4a6d54-52b5-4893-b5f6-93917ac88ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:14:44,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea4a6d54-52b5-4893-b5f6-93917ac88ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:14:44,117] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:14:44,118] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:14:44,118] [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
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	79.1177	409	1012	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.8688	399	1012	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	78.8552	402	1012	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.6651	402	1012	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	78.4528	325	1012	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	78.4435	295	1012	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	78.4127	355	1012	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	78.2882	364	1012	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.1899	313	1012	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	78.157	322	1012	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	78.1466	291	1012	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	78.1419	320	1012	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	78.1065	290	1012	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.9493	295	1012	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	77.9335	301	1012	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	77.915	293	1012	95	below_threshold
Sphingomonas jeddahensis	strain=G39	GCA_001981525.1	1915074	1915074	type	True	77.8473	242	1012	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	77.7937	248	1012	95	below_threshold
Sphingobium algorifonticola	strain=TLA-22	GCA_004005485.1	2008318	2008318	type	True	77.7513	221	1012	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.6905	266	1012	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	77.6713	282	1012	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.6296	257	1012	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.5665	258	1012	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.4955	284	1012	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	77.4093	213	1012	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.3768	262	1012	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	77.3744	242	1012	95	below_threshold
Sphingomonas aerophila	strain=DSM 100044	GCA_014199305.1	1344948	1344948	type	True	77.2412	193	1012	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	77.2239	190	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:14:44,120] [INFO] DFAST Taxonomy check result was written to GCA_021732885.1_ASM2173288v1_genomic.fna/tc_result.tsv
[2023-06-29 20:14:44,121] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:14:44,121] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:14:44,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea4a6d54-52b5-4893-b5f6-93917ac88ff2/dqc_reference/checkm_data
[2023-06-29 20:14:44,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:14:44,165] [INFO] Task started: CheckM
[2023-06-29 20:14:44,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021732885.1_ASM2173288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021732885.1_ASM2173288v1_genomic.fna/checkm_input GCA_021732885.1_ASM2173288v1_genomic.fna/checkm_result
[2023-06-29 20:15:15,806] [INFO] Task succeeded: CheckM
[2023-06-29 20:15:15,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.80%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 20:15:15,832] [INFO] ===== Completeness check finished =====
[2023-06-29 20:15:15,833] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:15:15,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021732885.1_ASM2173288v1_genomic.fna/markers.fasta)
[2023-06-29 20:15:15,834] [INFO] Task started: Blastn
[2023-06-29 20:15:15,834] [INFO] Running command: blastn -query GCA_021732885.1_ASM2173288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea4a6d54-52b5-4893-b5f6-93917ac88ff2/dqc_reference/reference_markers_gtdb.fasta -out GCA_021732885.1_ASM2173288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:15:16,949] [INFO] Task succeeded: Blastn
[2023-06-29 20:15:16,954] [INFO] Selected 14 target genomes.
[2023-06-29 20:15:16,954] [INFO] Target genome list was writen to GCA_021732885.1_ASM2173288v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:15:16,959] [INFO] Task started: fastANI
[2023-06-29 20:15:16,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg5171c7a7-faab-496c-a1ed-0d586f1d854d/GCA_021732885.1_ASM2173288v1_genomic.fna.gz --refList GCA_021732885.1_ASM2173288v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021732885.1_ASM2173288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:15:26,717] [INFO] Task succeeded: fastANI
[2023-06-29 20:15:26,734] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:15:26,734] [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_001464615.1	s__Sphingomonas sp001464615	94.9876	837	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.17	95.17	0.82	0.82	2	-
GCA_002281535.1	s__Sphingomonas sp002281535	82.531	643	1012	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	81.515	590	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.55	97.47	0.91	0.90	3	-
GCA_002281485.1	s__Sphingomonas sp002281485	81.079	495	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083655.1	s__Sphingomonas sp002083655	80.8903	569	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556185.1	s__Sphingomonas sp001556185	79.9801	470	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.51	96.51	0.87	0.87	2	-
GCA_002863155.1	s__Sphingomonas sp002863155	79.6433	441	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884945.1	s__Sphingomonas sp903884945	78.5488	366	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403415.1	s__Sphingomonas sp002403415	78.2688	340	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.53	96.29	0.87	0.85	4	-
GCF_000764535.1	s__Sphingomonas taxi	78.2022	312	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_013344685.1	s__Sphingomonas sp013344685	78.1272	320	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001981525.1	s__Sphingomonas jeddahensis	77.847	242	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197685.1	s__Sphingomonas dokdonensis	77.8168	247	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109205.1	s__Sphingomonas sp900109205	77.6465	249	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-29 20:15:26,736] [INFO] GTDB search result was written to GCA_021732885.1_ASM2173288v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:15:26,737] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:15:26,741] [INFO] DFAST_QC result json was written to GCA_021732885.1_ASM2173288v1_genomic.fna/dqc_result.json
[2023-06-29 20:15:26,741] [INFO] DFAST_QC completed!
[2023-06-29 20:15:26,741] [INFO] Total running time: 0h1m18s