[2024-01-25 18:52:20,436] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:20,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:20,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg6db15dd8-52e9-4b9c-a6f1-7c0cb516eae9/dqc_reference
[2024-01-25 18:52:21,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:21,554] [INFO] Task started: Prodigal
[2024-01-25 18:52:21,554] [INFO] Running command: gunzip -c /var/lib/cwl/stge5c91cfa-189e-42b3-9af6-55d0faf34ef9/GCF_026157155.1_ASM2615715v1_genomic.fna.gz | prodigal -d GCF_026157155.1_ASM2615715v1_genomic.fna/cds.fna -a GCF_026157155.1_ASM2615715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:27,163] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:27,164] [INFO] Task started: HMMsearch
[2024-01-25 18:52:27,164] [INFO] Running command: hmmsearch --tblout GCF_026157155.1_ASM2615715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6db15dd8-52e9-4b9c-a6f1-7c0cb516eae9/dqc_reference/reference_markers.hmm GCF_026157155.1_ASM2615715v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:27,350] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:27,351] [INFO] Found 6/6 markers.
[2024-01-25 18:52:27,371] [INFO] Query marker FASTA was written to GCF_026157155.1_ASM2615715v1_genomic.fna/markers.fasta
[2024-01-25 18:52:27,372] [INFO] Task started: Blastn
[2024-01-25 18:52:27,372] [INFO] Running command: blastn -query GCF_026157155.1_ASM2615715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db15dd8-52e9-4b9c-a6f1-7c0cb516eae9/dqc_reference/reference_markers.fasta -out GCF_026157155.1_ASM2615715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:28,312] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:28,315] [INFO] Selected 15 target genomes.
[2024-01-25 18:52:28,315] [INFO] Target genome list was writen to GCF_026157155.1_ASM2615715v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:28,325] [INFO] Task started: fastANI
[2024-01-25 18:52:28,325] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c91cfa-189e-42b3-9af6-55d0faf34ef9/GCF_026157155.1_ASM2615715v1_genomic.fna.gz --refList GCF_026157155.1_ASM2615715v1_genomic.fna/target_genomes.txt --output GCF_026157155.1_ASM2615715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:37,394] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:37,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6db15dd8-52e9-4b9c-a6f1-7c0cb516eae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:37,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6db15dd8-52e9-4b9c-a6f1-7c0cb516eae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:37,404] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:52:37,404] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:37,404] [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
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	99.9996	746	748	95	conclusive
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	86.4717	630	748	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	86.397	629	748	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	80.2027	423	748	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	79.5513	402	748	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	79.3262	422	748	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.257	374	748	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.6535	310	748	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.3695	277	748	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.9862	294	748	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	77.8976	261	748	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	77.7722	260	748	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	77.5871	284	748	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.5597	315	748	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	77.5586	251	748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:37,405] [INFO] DFAST Taxonomy check result was written to GCF_026157155.1_ASM2615715v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:37,406] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:37,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:37,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6db15dd8-52e9-4b9c-a6f1-7c0cb516eae9/dqc_reference/checkm_data
[2024-01-25 18:52:37,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:37,431] [INFO] Task started: CheckM
[2024-01-25 18:52:37,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026157155.1_ASM2615715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026157155.1_ASM2615715v1_genomic.fna/checkm_input GCF_026157155.1_ASM2615715v1_genomic.fna/checkm_result
[2024-01-25 18:52:57,530] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:57,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:57,551] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:57,551] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:57,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026157155.1_ASM2615715v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:57,552] [INFO] Task started: Blastn
[2024-01-25 18:52:57,552] [INFO] Running command: blastn -query GCF_026157155.1_ASM2615715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db15dd8-52e9-4b9c-a6f1-7c0cb516eae9/dqc_reference/reference_markers_gtdb.fasta -out GCF_026157155.1_ASM2615715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:59,424] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:59,427] [INFO] Selected 26 target genomes.
[2024-01-25 18:52:59,428] [INFO] Target genome list was writen to GCF_026157155.1_ASM2615715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:59,455] [INFO] Task started: fastANI
[2024-01-25 18:52:59,455] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c91cfa-189e-42b3-9af6-55d0faf34ef9/GCF_026157155.1_ASM2615715v1_genomic.fna.gz --refList GCF_026157155.1_ASM2615715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026157155.1_ASM2615715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:15,363] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:15,379] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:53:15,379] [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_014195685.1	s__Sphingomicrobium lutaoense	80.2296	421	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711715.1	s__Sphingomicrobium astaxanthinifaciens	79.5383	403	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	79.4396	380	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	79.3053	384	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	79.1837	380	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001055.1	s__Sphingomicrobium sp004282935	78.8972	333	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	78.8884	268	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	78.8854	355	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396785.1	s__Sphingomicrobium lutea	78.6714	304	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	78.6139	313	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	78.5404	300	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.4818	295	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	78.3882	275	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	78.3597	275	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816785.1	s__Sphingomicrobium sp013816785	78.2749	298	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	78.1297	347	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	78.0456	328	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCA_017744835.1	s__Sphingomonas sp017744835	78.0155	334	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883305.1	s__Allosphingosinicella sp005883305	77.9861	303	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489495.1	s__Sphingomicrobium daechungense	77.8901	230	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	77.8239	311	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	77.7866	316	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122655.1	s__Sphingomonas sp018122655	77.7055	254	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380205.1	s__Parasphingopyxis sp014380205	77.6556	242	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	77.6102	207	748	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_011762125.1	s__Sphingopyxis panaciterrae	77.5581	251	748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:15,386] [INFO] GTDB search result was written to GCF_026157155.1_ASM2615715v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:15,386] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:15,390] [INFO] DFAST_QC result json was written to GCF_026157155.1_ASM2615715v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:15,391] [INFO] DFAST_QC completed!
[2024-01-25 18:53:15,391] [INFO] Total running time: 0h0m55s