[2024-01-24 13:13:34,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:34,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:34,456] [INFO] DQC Reference Directory: /var/lib/cwl/stg0958262c-8c66-4e55-bb10-7daca685afa5/dqc_reference
[2024-01-24 13:13:35,669] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:35,669] [INFO] Task started: Prodigal
[2024-01-24 13:13:35,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg523f8479-8d9b-44b6-b0b3-21f631a8b3b2/GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/cds.fna -a GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:48,187] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:48,187] [INFO] Task started: HMMsearch
[2024-01-24 13:13:48,187] [INFO] Running command: hmmsearch --tblout GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0958262c-8c66-4e55-bb10-7daca685afa5/dqc_reference/reference_markers.hmm GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:48,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:48,447] [INFO] Found 6/6 markers.
[2024-01-24 13:13:48,483] [INFO] Query marker FASTA was written to GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:48,483] [INFO] Task started: Blastn
[2024-01-24 13:13:48,483] [INFO] Running command: blastn -query GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0958262c-8c66-4e55-bb10-7daca685afa5/dqc_reference/reference_markers.fasta -out GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:49,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:49,521] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:49,521] [INFO] Target genome list was writen to GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:49,532] [INFO] Task started: fastANI
[2024-01-24 13:13:49,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg523f8479-8d9b-44b6-b0b3-21f631a8b3b2/GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna.gz --refList GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:06,417] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:06,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0958262c-8c66-4e55-bb10-7daca685afa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:06,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0958262c-8c66-4e55-bb10-7daca685afa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:06,435] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:06,435] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:06,436] [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 jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	100.0	1350	1350	95	conclusive
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.8931	627	1350	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.5026	537	1350	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	79.3193	488	1350	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.2752	465	1350	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.1724	449	1350	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	79.0094	387	1350	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.9852	507	1350	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.8895	516	1350	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.8363	506	1350	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	78.8249	498	1350	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.8	492	1350	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.6585	417	1350	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.6474	402	1350	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.4557	373	1350	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.3586	362	1350	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.3478	390	1350	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.3465	393	1350	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	78.0053	225	1350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:06,438] [INFO] DFAST Taxonomy check result was written to GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:14:06,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:06,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:06,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0958262c-8c66-4e55-bb10-7daca685afa5/dqc_reference/checkm_data
[2024-01-24 13:14:06,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:06,485] [INFO] Task started: CheckM
[2024-01-24 13:14:06,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/checkm_input GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:14:45,555] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:45,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:45,573] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:45,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:45,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:14:45,574] [INFO] Task started: Blastn
[2024-01-24 13:14:45,574] [INFO] Running command: blastn -query GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0958262c-8c66-4e55-bb10-7daca685afa5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:47,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:47,435] [INFO] Selected 24 target genomes.
[2024-01-24 13:14:47,435] [INFO] Target genome list was writen to GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:47,460] [INFO] Task started: fastANI
[2024-01-24 13:14:47,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg523f8479-8d9b-44b6-b0b3-21f631a8b3b2/GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna.gz --refList GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:04,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:04,882] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:04,882] [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_900113315.1	s__Sphingomonas_G jatrophae	100.0	1350	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009739515.1	s__Sphingomonas_G sp009739515	79.8739	628	1350	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_003034225.1	s__Sphingomonas_E fennica	79.4976	537	1350	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_000383095.1	s__Sphingomonas_N sp000383095	79.4483	464	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863195.1	s__XMGL2 sp018863195	79.3205	467	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__XMGL2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762195.1	s__Sphingomonas_N oligoaromativorans	79.3174	488	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	79.2642	465	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	79.1727	448	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761305.1	s__Sphingomonas_I vulcanisoli	79.0197	386	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	78.9335	442	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.9086	388	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871605.1	s__Sphingomonas_N sp903871605	78.8906	466	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.8284	507	1350	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_000764535.1	s__Sphingomonas taxi	78.771	496	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_004341505.2	s__Sphingomonas sp004341505	78.7391	448	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_009753715.1	s__Sphingomonas_B horti	78.6621	416	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	78.5984	382	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	78.5659	405	1350	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_000974765.1	s__Sphingomonas_B changbaiensis	78.5469	392	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	78.4326	395	1350	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_004564275.1	s__Allosphingosinicella parva	78.392	385	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.3377	365	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240865.1	s__Sphingomonas_B sp018240865	78.3197	363	1350	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_011320075.1	s__Allosphingosinicella sp011320075	78.0829	384	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:04,884] [INFO] GTDB search result was written to GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:04,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:04,889] [INFO] DFAST_QC result json was written to GCF_900113315.1_IMG-taxon_2654588199_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:15:04,889] [INFO] DFAST_QC completed!
[2024-01-24 13:15:04,890] [INFO] Total running time: 0h1m30s