[2024-01-24 14:30:59,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg2752bb99-5f38-4e58-84be-4a8522df41df/dqc_reference
[2024-01-24 14:31:00,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,874] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,874] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7400b14-0950-4485-a523-4bd77006be4c/GCF_014199335.1_ASM1419933v1_genomic.fna.gz | prodigal -d GCF_014199335.1_ASM1419933v1_genomic.fna/cds.fna -a GCF_014199335.1_ASM1419933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:12,238] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:12,238] [INFO] Task started: HMMsearch
[2024-01-24 14:31:12,239] [INFO] Running command: hmmsearch --tblout GCF_014199335.1_ASM1419933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2752bb99-5f38-4e58-84be-4a8522df41df/dqc_reference/reference_markers.hmm GCF_014199335.1_ASM1419933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:12,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:12,527] [INFO] Found 6/6 markers.
[2024-01-24 14:31:12,558] [INFO] Query marker FASTA was written to GCF_014199335.1_ASM1419933v1_genomic.fna/markers.fasta
[2024-01-24 14:31:12,559] [INFO] Task started: Blastn
[2024-01-24 14:31:12,559] [INFO] Running command: blastn -query GCF_014199335.1_ASM1419933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2752bb99-5f38-4e58-84be-4a8522df41df/dqc_reference/reference_markers.fasta -out GCF_014199335.1_ASM1419933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:13,496] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:13,499] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:13,500] [INFO] Target genome list was writen to GCF_014199335.1_ASM1419933v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:13,507] [INFO] Task started: fastANI
[2024-01-24 14:31:13,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7400b14-0950-4485-a523-4bd77006be4c/GCF_014199335.1_ASM1419933v1_genomic.fna.gz --refList GCF_014199335.1_ASM1419933v1_genomic.fna/target_genomes.txt --output GCF_014199335.1_ASM1419933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:27,531] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:27,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2752bb99-5f38-4e58-84be-4a8522df41df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:27,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2752bb99-5f38-4e58-84be-4a8522df41df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:27,548] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:27,548] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:27,549] [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
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	100.0	1139	1141	95	conclusive
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	79.8999	499	1141	95	below_threshold
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	79.7506	536	1141	95	below_threshold
Stakelama pacifica	strain=DSM 25059	GCA_004361835.1	517720	517720	type	True	79.6828	543	1141	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	79.1787	475	1141	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.957	452	1141	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.5965	406	1141	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.3529	402	1141	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.3244	383	1141	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	78.1961	408	1141	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.1704	379	1141	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.1306	401	1141	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	78.113	409	1141	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	78.1077	377	1141	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.0517	359	1141	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.9008	329	1141	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.6075	292	1141	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	77.544	285	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:27,550] [INFO] DFAST Taxonomy check result was written to GCF_014199335.1_ASM1419933v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:27,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:27,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:27,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2752bb99-5f38-4e58-84be-4a8522df41df/dqc_reference/checkm_data
[2024-01-24 14:31:27,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:27,592] [INFO] Task started: CheckM
[2024-01-24 14:31:27,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199335.1_ASM1419933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199335.1_ASM1419933v1_genomic.fna/checkm_input GCF_014199335.1_ASM1419933v1_genomic.fna/checkm_result
[2024-01-24 14:32:03,631] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:03,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:03,656] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:03,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:03,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199335.1_ASM1419933v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:03,657] [INFO] Task started: Blastn
[2024-01-24 14:32:03,658] [INFO] Running command: blastn -query GCF_014199335.1_ASM1419933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2752bb99-5f38-4e58-84be-4a8522df41df/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199335.1_ASM1419933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:05,284] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:05,289] [INFO] Selected 20 target genomes.
[2024-01-24 14:32:05,289] [INFO] Target genome list was writen to GCF_014199335.1_ASM1419933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:05,304] [INFO] Task started: fastANI
[2024-01-24 14:32:05,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7400b14-0950-4485-a523-4bd77006be4c/GCF_014199335.1_ASM1419933v1_genomic.fna.gz --refList GCF_014199335.1_ASM1419933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199335.1_ASM1419933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:20,088] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:20,108] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:20,108] [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_014199335.1	s__Sphingomonas sediminis	100.0	1139	1141	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_018122655.1	s__Sphingomonas sp018122655	79.857	550	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361835.1	s__Sphingomonas pacifica	79.693	541	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	-
GCF_003171655.1	s__Sphingomonas portus	79.1842	475	1141	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	78.9868	374	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_011057975.1	s__Sphingomonas sp011057975	78.9771	450	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707985.1	s__Sphingomonas sp002707985	78.9325	431	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	78.6304	427	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833215.1	s__Sphingomonas sp007833215	78.607	405	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	78.2043	370	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	78.2007	402	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_004792695.1	s__Sphingomonas naasensis	78.1963	408	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003355005.1	s__Sphingomonas sp003355005	78.1397	369	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199325.1	s__Sphingomonas yantingensis	78.1177	376	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	-
GCF_014641735.1	s__Sphingomonas metalli	78.0516	359	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	78.037	387	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_014489075.1	s__Sphingomonas sp014489075	78.0291	387	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498785.1	s__Sphingomonas sp902498785	77.9612	347	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304615.1	s__Sphingomonas sp017304615	77.8718	367	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	77.5107	298	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:20,110] [INFO] GTDB search result was written to GCF_014199335.1_ASM1419933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:20,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:20,116] [INFO] DFAST_QC result json was written to GCF_014199335.1_ASM1419933v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:20,116] [INFO] DFAST_QC completed!
[2024-01-24 14:32:20,116] [INFO] Total running time: 0h1m21s