[2024-01-24 12:45:10,014] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,017] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,017] [INFO] DQC Reference Directory: /var/lib/cwl/stg83d2e745-ff2c-4a14-8f64-1645b90a93af/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,083] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgb406d862-3ee1-4677-9316-59d2829385f9/GCF_014636175.1_ASM1463617v1_genomic.fna.gz | prodigal -d GCF_014636175.1_ASM1463617v1_genomic.fna/cds.fna -a GCF_014636175.1_ASM1463617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:24,542] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:24,543] [INFO] Task started: HMMsearch
[2024-01-24 12:45:24,543] [INFO] Running command: hmmsearch --tblout GCF_014636175.1_ASM1463617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83d2e745-ff2c-4a14-8f64-1645b90a93af/dqc_reference/reference_markers.hmm GCF_014636175.1_ASM1463617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:24,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:24,814] [INFO] Found 6/6 markers.
[2024-01-24 12:45:24,849] [INFO] Query marker FASTA was written to GCF_014636175.1_ASM1463617v1_genomic.fna/markers.fasta
[2024-01-24 12:45:24,849] [INFO] Task started: Blastn
[2024-01-24 12:45:24,849] [INFO] Running command: blastn -query GCF_014636175.1_ASM1463617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83d2e745-ff2c-4a14-8f64-1645b90a93af/dqc_reference/reference_markers.fasta -out GCF_014636175.1_ASM1463617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:25,700] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:25,703] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:25,704] [INFO] Target genome list was writen to GCF_014636175.1_ASM1463617v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:25,727] [INFO] Task started: fastANI
[2024-01-24 12:45:25,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgb406d862-3ee1-4677-9316-59d2829385f9/GCF_014636175.1_ASM1463617v1_genomic.fna.gz --refList GCF_014636175.1_ASM1463617v1_genomic.fna/target_genomes.txt --output GCF_014636175.1_ASM1463617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:39,207] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:39,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83d2e745-ff2c-4a14-8f64-1645b90a93af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:39,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83d2e745-ff2c-4a14-8f64-1645b90a93af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:39,220] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:39,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:39,220] [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 psychrolutea	strain=CGMCC 1.10106	GCA_014636175.1	1259676	1259676	type	True	100.0	1223	1224	95	conclusive
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	82.7419	786	1224	95	below_threshold
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	82.7071	754	1224	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.5718	608	1224	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	80.2481	558	1224	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	80.2051	563	1224	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.881	587	1224	95	below_threshold
Sphingomonas aliaeris	strain=DH-S5	GCA_016743815.1	2759526	2759526	type	True	79.499	528	1224	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.318	530	1224	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	79.0858	514	1224	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	78.8043	446	1224	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.5472	440	1224	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.4033	452	1224	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.054	397	1224	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.8197	340	1224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:39,222] [INFO] DFAST Taxonomy check result was written to GCF_014636175.1_ASM1463617v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:39,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:39,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:39,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83d2e745-ff2c-4a14-8f64-1645b90a93af/dqc_reference/checkm_data
[2024-01-24 12:45:39,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:39,268] [INFO] Task started: CheckM
[2024-01-24 12:45:39,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636175.1_ASM1463617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636175.1_ASM1463617v1_genomic.fna/checkm_input GCF_014636175.1_ASM1463617v1_genomic.fna/checkm_result
[2024-01-24 12:46:15,527] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:15,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:15,555] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:15,555] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:15,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636175.1_ASM1463617v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:15,557] [INFO] Task started: Blastn
[2024-01-24 12:46:15,557] [INFO] Running command: blastn -query GCF_014636175.1_ASM1463617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83d2e745-ff2c-4a14-8f64-1645b90a93af/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636175.1_ASM1463617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:17,223] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:17,228] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:17,229] [INFO] Target genome list was writen to GCF_014636175.1_ASM1463617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:17,258] [INFO] Task started: fastANI
[2024-01-24 12:46:17,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgb406d862-3ee1-4677-9316-59d2829385f9/GCF_014636175.1_ASM1463617v1_genomic.fna.gz --refList GCF_014636175.1_ASM1463617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636175.1_ASM1463617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:26,066] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:26,080] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:26,081] [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_014636175.1	s__Sphingomonas psychrolutea	100.0	1223	1224	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_013374095.1	s__Sphingomonas sp013374095	86.6338	885	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439055.1	s__Sphingomonas glacialis_A	82.8706	794	1224	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	82.8192	767	1224	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	82.7432	785	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_000241465.1	s__Sphingomonas echinoides	82.7284	752	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.65	96.65	0.85	0.85	2	-
GCF_000797515.1	s__Sphingomonas sp000797515	82.5378	660	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.00	97.12	0.86	0.75	5	-
GCF_001717955.1	s__Sphingomonas panacis	80.1719	566	1224	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 12:46:26,083] [INFO] GTDB search result was written to GCF_014636175.1_ASM1463617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:26,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:26,088] [INFO] DFAST_QC result json was written to GCF_014636175.1_ASM1463617v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:26,088] [INFO] DFAST_QC completed!
[2024-01-24 12:46:26,088] [INFO] Total running time: 0h1m16s