[2024-01-25 18:08:20,513] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:20,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:20,515] [INFO] DQC Reference Directory: /var/lib/cwl/stgd566a46e-3175-4b9a-a580-b068b4efd5d1/dqc_reference
[2024-01-25 18:08:21,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:21,683] [INFO] Task started: Prodigal
[2024-01-25 18:08:21,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg58f2ef3c-c96c-43da-99f2-cb25419dcc00/GCF_014202205.1_ASM1420220v1_genomic.fna.gz | prodigal -d GCF_014202205.1_ASM1420220v1_genomic.fna/cds.fna -a GCF_014202205.1_ASM1420220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:29,794] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:29,795] [INFO] Task started: HMMsearch
[2024-01-25 18:08:29,795] [INFO] Running command: hmmsearch --tblout GCF_014202205.1_ASM1420220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd566a46e-3175-4b9a-a580-b068b4efd5d1/dqc_reference/reference_markers.hmm GCF_014202205.1_ASM1420220v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:29,991] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:29,993] [INFO] Found 6/6 markers.
[2024-01-25 18:08:30,021] [INFO] Query marker FASTA was written to GCF_014202205.1_ASM1420220v1_genomic.fna/markers.fasta
[2024-01-25 18:08:30,021] [INFO] Task started: Blastn
[2024-01-25 18:08:30,022] [INFO] Running command: blastn -query GCF_014202205.1_ASM1420220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd566a46e-3175-4b9a-a580-b068b4efd5d1/dqc_reference/reference_markers.fasta -out GCF_014202205.1_ASM1420220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:30,874] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:30,877] [INFO] Selected 21 target genomes.
[2024-01-25 18:08:30,878] [INFO] Target genome list was writen to GCF_014202205.1_ASM1420220v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:30,885] [INFO] Task started: fastANI
[2024-01-25 18:08:30,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg58f2ef3c-c96c-43da-99f2-cb25419dcc00/GCF_014202205.1_ASM1420220v1_genomic.fna.gz --refList GCF_014202205.1_ASM1420220v1_genomic.fna/target_genomes.txt --output GCF_014202205.1_ASM1420220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:44,213] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:44,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd566a46e-3175-4b9a-a580-b068b4efd5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:44,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd566a46e-3175-4b9a-a580-b068b4efd5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:44,225] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:08:44,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:44,226] [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
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	100.0	1065	1066	95	conclusive
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	99.9936	1053	1066	95	conclusive
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	77.581	200	1066	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	77.2607	115	1066	95	below_threshold
Sphingosinicella soli	strain=DSM 17328	GCA_014199685.1	333708	333708	type	True	77.2047	224	1066	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	77.1036	161	1066	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	77.1013	168	1066	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	77.0096	183	1066	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	76.9879	214	1066	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_014197135.1	1646122	1646122	type	True	76.9872	177	1066	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	76.9659	114	1066	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	76.9153	153	1066	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	76.8921	190	1066	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	76.8712	86	1066	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	76.8034	107	1066	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	76.7598	179	1066	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.7015	185	1066	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	76.4606	118	1066	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	76.3855	134	1066	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.6663	70	1066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:44,227] [INFO] DFAST Taxonomy check result was written to GCF_014202205.1_ASM1420220v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:44,228] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:44,228] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:44,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd566a46e-3175-4b9a-a580-b068b4efd5d1/dqc_reference/checkm_data
[2024-01-25 18:08:44,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:44,262] [INFO] Task started: CheckM
[2024-01-25 18:08:44,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202205.1_ASM1420220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202205.1_ASM1420220v1_genomic.fna/checkm_input GCF_014202205.1_ASM1420220v1_genomic.fna/checkm_result
[2024-01-25 18:09:10,787] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:10,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:10,807] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:10,807] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:10,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202205.1_ASM1420220v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:10,807] [INFO] Task started: Blastn
[2024-01-25 18:09:10,808] [INFO] Running command: blastn -query GCF_014202205.1_ASM1420220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd566a46e-3175-4b9a-a580-b068b4efd5d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202205.1_ASM1420220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:12,465] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:12,468] [INFO] Selected 20 target genomes.
[2024-01-25 18:09:12,468] [INFO] Target genome list was writen to GCF_014202205.1_ASM1420220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:12,490] [INFO] Task started: fastANI
[2024-01-25 18:09:12,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg58f2ef3c-c96c-43da-99f2-cb25419dcc00/GCF_014202205.1_ASM1420220v1_genomic.fna.gz --refList GCF_014202205.1_ASM1420220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202205.1_ASM1420220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:26,404] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:26,416] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:26,416] [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_000342165.1	s__Pacificimonas flava	99.9936	1053	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002211145.1	s__Pacificimonas flava_A	78.9993	399	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375465.1	s__Pacificimonas sp002375465	77.7419	289	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019204005.1	s__Pacificimonas sp019204005	77.624	256	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634215.1	s__Sphingosinicella microcystinivorans	77.613	198	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_016793845.1	s__Sphingosinicella sp016793845	77.4471	188	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199685.1	s__Sphingosinicella soli	77.1814	226	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739895.2	s__Sphingomonas paucimobilis	77.1191	160	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
GCF_002355275.1	s__Rhizorhabdus dicambivorans	77.0586	186	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.99	99.99	1.00	0.99	3	-
GCF_014197135.1	s__Sphingomonas zeae	77.0014	176	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001890385.1	s__Tardibacter chloracetimidivorans	76.9437	115	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tardibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	76.9078	218	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	76.8794	191	1066	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_001428605.1	s__Rhizorhabdus sp001428605	76.8665	191	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	76.8598	169	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248935.1	s__Sphingobium sp003248935	76.8374	171	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282895.1	s__Sphingomonas sp000282895	76.8248	167	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004005865.1	s__Rhizorhabdus crocodyli	76.7623	189	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297635.1	s__Rhizorhabdus sp004297635	76.4951	97	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.78	98.78	0.98	0.98	2	-
GCF_009363255.1	s__Roseivivax sp009363255	76.4375	56	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:26,418] [INFO] GTDB search result was written to GCF_014202205.1_ASM1420220v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:26,418] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:26,422] [INFO] DFAST_QC result json was written to GCF_014202205.1_ASM1420220v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:26,423] [INFO] DFAST_QC completed!
[2024-01-25 18:09:26,423] [INFO] Total running time: 0h1m6s