[2024-01-25 19:38:20,405] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:20,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:20,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg36b93e97-6673-43a2-9c97-61d1155e271d/dqc_reference
[2024-01-25 19:38:21,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:21,538] [INFO] Task started: Prodigal
[2024-01-25 19:38:21,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg82761aac-e6fc-4439-bf30-6232149a7fee/GCF_003171655.1_ASM317165v1_genomic.fna.gz | prodigal -d GCF_003171655.1_ASM317165v1_genomic.fna/cds.fna -a GCF_003171655.1_ASM317165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:31,739] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:31,739] [INFO] Task started: HMMsearch
[2024-01-25 19:38:31,739] [INFO] Running command: hmmsearch --tblout GCF_003171655.1_ASM317165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36b93e97-6673-43a2-9c97-61d1155e271d/dqc_reference/reference_markers.hmm GCF_003171655.1_ASM317165v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:31,953] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:31,954] [INFO] Found 6/6 markers.
[2024-01-25 19:38:31,983] [INFO] Query marker FASTA was written to GCF_003171655.1_ASM317165v1_genomic.fna/markers.fasta
[2024-01-25 19:38:31,984] [INFO] Task started: Blastn
[2024-01-25 19:38:31,984] [INFO] Running command: blastn -query GCF_003171655.1_ASM317165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36b93e97-6673-43a2-9c97-61d1155e271d/dqc_reference/reference_markers.fasta -out GCF_003171655.1_ASM317165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:32,846] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:32,849] [INFO] Selected 20 target genomes.
[2024-01-25 19:38:32,849] [INFO] Target genome list was writen to GCF_003171655.1_ASM317165v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:32,861] [INFO] Task started: fastANI
[2024-01-25 19:38:32,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg82761aac-e6fc-4439-bf30-6232149a7fee/GCF_003171655.1_ASM317165v1_genomic.fna.gz --refList GCF_003171655.1_ASM317165v1_genomic.fna/target_genomes.txt --output GCF_003171655.1_ASM317165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:49,612] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:49,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36b93e97-6673-43a2-9c97-61d1155e271d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:49,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36b93e97-6673-43a2-9c97-61d1155e271d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:49,624] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:49,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:49,625] [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
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	100.0	1274	1275	95	conclusive
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	84.2841	815	1275	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.6417	577	1275	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.6027	571	1275	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	79.5206	604	1275	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.4426	538	1275	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.1466	513	1275	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	79.1391	574	1275	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	79.1314	534	1275	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.1045	525	1275	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.0962	472	1275	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	79.0829	539	1275	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	79.0821	515	1275	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.0288	521	1275	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.0218	525	1275	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.6828	464	1275	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.6528	487	1275	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.3519	400	1275	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.0396	343	1275	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.7031	296	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:49,626] [INFO] DFAST Taxonomy check result was written to GCF_003171655.1_ASM317165v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:49,626] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:49,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:49,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36b93e97-6673-43a2-9c97-61d1155e271d/dqc_reference/checkm_data
[2024-01-25 19:38:49,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:49,670] [INFO] Task started: CheckM
[2024-01-25 19:38:49,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003171655.1_ASM317165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003171655.1_ASM317165v1_genomic.fna/checkm_input GCF_003171655.1_ASM317165v1_genomic.fna/checkm_result
[2024-01-25 19:39:22,932] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:22,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:22,956] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:22,957] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:22,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003171655.1_ASM317165v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:22,957] [INFO] Task started: Blastn
[2024-01-25 19:39:22,957] [INFO] Running command: blastn -query GCF_003171655.1_ASM317165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36b93e97-6673-43a2-9c97-61d1155e271d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003171655.1_ASM317165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:24,657] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:24,660] [INFO] Selected 11 target genomes.
[2024-01-25 19:39:24,660] [INFO] Target genome list was writen to GCF_003171655.1_ASM317165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:24,668] [INFO] Task started: fastANI
[2024-01-25 19:39:24,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg82761aac-e6fc-4439-bf30-6232149a7fee/GCF_003171655.1_ASM317165v1_genomic.fna.gz --refList GCF_003171655.1_ASM317165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003171655.1_ASM317165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:34,047] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:34,058] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:34,058] [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_003171655.1	s__Sphingomonas portus	100.0	1274	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002707985.1	s__Sphingomonas sp002707985	91.4902	901	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	84.3083	813	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	80.2289	604	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826325.1	s__Sphingomonas sp902826325	79.797	424	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_004792695.1	s__Sphingomonas naasensis	79.612	570	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000712135.1	s__Sphingomonas sp000712135	79.2177	533	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	79.1735	547	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226955.1	s__Sphingomonas elodea_A	79.0716	511	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	79.0115	523	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	77.6585	300	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:34,059] [INFO] GTDB search result was written to GCF_003171655.1_ASM317165v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:34,060] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:34,063] [INFO] DFAST_QC result json was written to GCF_003171655.1_ASM317165v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:34,063] [INFO] DFAST_QC completed!
[2024-01-25 19:39:34,063] [INFO] Total running time: 0h1m14s