[2024-01-24 12:53:36,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg587fc144-6ec3-4887-a6a6-a4dcd0fe437f/dqc_reference
[2024-01-24 12:53:38,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,170] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,170] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e05ba7-4c23-45d0-9d22-443ae0153c9c/GCF_009789535.1_ASM978953v1_genomic.fna.gz | prodigal -d GCF_009789535.1_ASM978953v1_genomic.fna/cds.fna -a GCF_009789535.1_ASM978953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:51,163] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:51,164] [INFO] Task started: HMMsearch
[2024-01-24 12:53:51,164] [INFO] Running command: hmmsearch --tblout GCF_009789535.1_ASM978953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg587fc144-6ec3-4887-a6a6-a4dcd0fe437f/dqc_reference/reference_markers.hmm GCF_009789535.1_ASM978953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:51,419] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:51,421] [INFO] Found 6/6 markers.
[2024-01-24 12:53:51,459] [INFO] Query marker FASTA was written to GCF_009789535.1_ASM978953v1_genomic.fna/markers.fasta
[2024-01-24 12:53:51,459] [INFO] Task started: Blastn
[2024-01-24 12:53:51,459] [INFO] Running command: blastn -query GCF_009789535.1_ASM978953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg587fc144-6ec3-4887-a6a6-a4dcd0fe437f/dqc_reference/reference_markers.fasta -out GCF_009789535.1_ASM978953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:52,437] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:52,441] [INFO] Selected 19 target genomes.
[2024-01-24 12:53:52,441] [INFO] Target genome list was writen to GCF_009789535.1_ASM978953v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:52,449] [INFO] Task started: fastANI
[2024-01-24 12:53:52,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e05ba7-4c23-45d0-9d22-443ae0153c9c/GCF_009789535.1_ASM978953v1_genomic.fna.gz --refList GCF_009789535.1_ASM978953v1_genomic.fna/target_genomes.txt --output GCF_009789535.1_ASM978953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:08,638] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:08,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg587fc144-6ec3-4887-a6a6-a4dcd0fe437f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:08,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg587fc144-6ec3-4887-a6a6-a4dcd0fe437f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:08,658] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:08,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:08,658] [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 carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	100.0	1358	1362	95	conclusive
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	99.988	1329	1362	95	conclusive
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	82.2604	739	1362	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	82.23	743	1362	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	81.9697	685	1362	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	81.9542	746	1362	95	below_threshold
Sphingomonas sanguinis	strain=NBRC 13937	GCA_001591005.1	33051	33051	suspected-type	True	81.9106	702	1362	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	81.9005	755	1362	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	81.8842	754	1362	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_014197135.1	1646122	1646122	type	True	81.7111	723	1362	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_013359795.1	1646122	1646122	type	True	81.6905	719	1362	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	81.4391	655	1362	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	81.2031	639	1362	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	80.7952	663	1362	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.151	644	1362	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	80.0502	607	1362	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.8918	655	1362	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.7945	619	1362	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.753	606	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:08,660] [INFO] DFAST Taxonomy check result was written to GCF_009789535.1_ASM978953v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:08,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:08,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:08,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg587fc144-6ec3-4887-a6a6-a4dcd0fe437f/dqc_reference/checkm_data
[2024-01-24 12:54:08,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:08,705] [INFO] Task started: CheckM
[2024-01-24 12:54:08,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009789535.1_ASM978953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009789535.1_ASM978953v1_genomic.fna/checkm_input GCF_009789535.1_ASM978953v1_genomic.fna/checkm_result
[2024-01-24 12:54:50,872] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:50,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:50,897] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:50,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:50,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009789535.1_ASM978953v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:50,898] [INFO] Task started: Blastn
[2024-01-24 12:54:50,898] [INFO] Running command: blastn -query GCF_009789535.1_ASM978953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg587fc144-6ec3-4887-a6a6-a4dcd0fe437f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009789535.1_ASM978953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:52,725] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:52,729] [INFO] Selected 14 target genomes.
[2024-01-24 12:54:52,730] [INFO] Target genome list was writen to GCF_009789535.1_ASM978953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:52,743] [INFO] Task started: fastANI
[2024-01-24 12:54:52,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e05ba7-4c23-45d0-9d22-443ae0153c9c/GCF_009789535.1_ASM978953v1_genomic.fna.gz --refList GCF_009789535.1_ASM978953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009789535.1_ASM978953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:05,235] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:05,260] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:05,260] [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_009789535.1	s__Sphingomonas carotinifaciens	100.0	1358	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.06	97.19	0.97	0.90	4	conclusive
GCF_014196255.1	s__Sphingomonas pseudosanguinis	82.239	742	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	82.1438	694	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	82.0222	663	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	81.9945	682	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739895.2	s__Sphingomonas paucimobilis	81.943	689	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
GCF_001591005.1	s__Sphingomonas sanguinis	81.8861	705	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.09	96.84	0.89	0.83	8	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	81.8844	652	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199595.1	s__Sphingomonas yabuuchiae	81.8818	754	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
GCF_014197135.1	s__Sphingomonas zeae	81.6853	726	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014641735.1	s__Sphingomonas metalli	81.4451	655	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	81.2099	638	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345355.1	s__Sphingomonas sp003345355	80.4589	564	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	79.5534	487	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:05,261] [INFO] GTDB search result was written to GCF_009789535.1_ASM978953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:05,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:05,265] [INFO] DFAST_QC result json was written to GCF_009789535.1_ASM978953v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:05,265] [INFO] DFAST_QC completed!
[2024-01-24 12:55:05,265] [INFO] Total running time: 0h1m28s