[2024-01-25 18:43:35,770] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,772] [INFO] DQC Reference Directory: /var/lib/cwl/stge8ae1c96-2ec3-4452-9fdd-d4632735fef1/dqc_reference
[2024-01-25 18:43:36,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,907] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgf25e98e9-cebd-4193-b503-2621338345c1/GCF_014490665.1_ASM1449066v1_genomic.fna.gz | prodigal -d GCF_014490665.1_ASM1449066v1_genomic.fna/cds.fna -a GCF_014490665.1_ASM1449066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:51,782] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:51,782] [INFO] Task started: HMMsearch
[2024-01-25 18:43:51,782] [INFO] Running command: hmmsearch --tblout GCF_014490665.1_ASM1449066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8ae1c96-2ec3-4452-9fdd-d4632735fef1/dqc_reference/reference_markers.hmm GCF_014490665.1_ASM1449066v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:52,035] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:52,036] [INFO] Found 6/6 markers.
[2024-01-25 18:43:52,076] [INFO] Query marker FASTA was written to GCF_014490665.1_ASM1449066v1_genomic.fna/markers.fasta
[2024-01-25 18:43:52,077] [INFO] Task started: Blastn
[2024-01-25 18:43:52,077] [INFO] Running command: blastn -query GCF_014490665.1_ASM1449066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ae1c96-2ec3-4452-9fdd-d4632735fef1/dqc_reference/reference_markers.fasta -out GCF_014490665.1_ASM1449066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:52,938] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:52,940] [INFO] Selected 15 target genomes.
[2024-01-25 18:43:52,941] [INFO] Target genome list was writen to GCF_014490665.1_ASM1449066v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:52,944] [INFO] Task started: fastANI
[2024-01-25 18:43:52,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgf25e98e9-cebd-4193-b503-2621338345c1/GCF_014490665.1_ASM1449066v1_genomic.fna.gz --refList GCF_014490665.1_ASM1449066v1_genomic.fna/target_genomes.txt --output GCF_014490665.1_ASM1449066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:06,427] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:06,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8ae1c96-2ec3-4452-9fdd-d4632735fef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:06,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8ae1c96-2ec3-4452-9fdd-d4632735fef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:06,438] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:06,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:06,438] [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 alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	100.0	1731	1732	95	conclusive
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	99.9806	1720	1732	95	conclusive
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	81.3273	718	1732	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	80.2496	636	1732	95	below_threshold
Sphingomonas aliaeris	strain=DH-S5	GCA_016743815.1	2759526	2759526	type	True	79.9382	652	1732	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	79.9137	577	1732	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.7262	591	1732	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.1573	527	1732	95	below_threshold
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	79.0893	515	1732	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.007	559	1732	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.9139	512	1732	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	78.8924	508	1732	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	78.8055	569	1732	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	78.7919	564	1732	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.7566	473	1732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:06,440] [INFO] DFAST Taxonomy check result was written to GCF_014490665.1_ASM1449066v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:06,442] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:06,442] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:06,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8ae1c96-2ec3-4452-9fdd-d4632735fef1/dqc_reference/checkm_data
[2024-01-25 18:44:06,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:06,492] [INFO] Task started: CheckM
[2024-01-25 18:44:06,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014490665.1_ASM1449066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014490665.1_ASM1449066v1_genomic.fna/checkm_input GCF_014490665.1_ASM1449066v1_genomic.fna/checkm_result
[2024-01-25 18:44:54,664] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:54,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:54,691] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:54,692] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:54,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014490665.1_ASM1449066v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:54,692] [INFO] Task started: Blastn
[2024-01-25 18:44:54,692] [INFO] Running command: blastn -query GCF_014490665.1_ASM1449066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ae1c96-2ec3-4452-9fdd-d4632735fef1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014490665.1_ASM1449066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:56,424] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:56,427] [INFO] Selected 13 target genomes.
[2024-01-25 18:44:56,427] [INFO] Target genome list was writen to GCF_014490665.1_ASM1449066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:56,441] [INFO] Task started: fastANI
[2024-01-25 18:44:56,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgf25e98e9-cebd-4193-b503-2621338345c1/GCF_014490665.1_ASM1449066v1_genomic.fna.gz --refList GCF_014490665.1_ASM1449066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014490665.1_ASM1449066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:09,723] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:09,733] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:09,734] [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_014490665.1	s__Sphingomonas alpina	100.0	1731	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000803065.1	s__Sphingomonas sp000803065	86.99	1329	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014171475.1	s__Sphingomonas alpina_A	85.956	1139	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423845.1	s__Sphingomonas sp001423845	81.1122	726	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884945.1	s__Sphingomonas sp903884945	80.5308	744	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241485.1	s__Sphingomonas sp000241485	80.3826	665	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653575.1	s__Sphingomonas glacialis	80.2679	634	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_016743815.1	s__Sphingomonas sp016743815	79.9546	650	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103265.1	s__Sphingomonas sp900103265	79.8577	559	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001717955.1	s__Sphingomonas panacis	79.7378	590	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281485.1	s__Sphingomonas sp002281485	79.6163	477	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789535.1	s__Sphingomonas carotinifaciens	79.137	519	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.06	97.19	0.97	0.90	4	-
GCF_002797435.1	s__Sphingomonas koreensis	78.7941	573	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:09,735] [INFO] GTDB search result was written to GCF_014490665.1_ASM1449066v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:09,736] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:09,739] [INFO] DFAST_QC result json was written to GCF_014490665.1_ASM1449066v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:09,739] [INFO] DFAST_QC completed!
[2024-01-25 18:45:09,739] [INFO] Total running time: 0h1m34s