[2024-01-24 13:01:08,278] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:08,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:08,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg11866d2d-2cee-48fd-9c50-d25fcff50014/dqc_reference
[2024-01-24 13:01:09,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:09,527] [INFO] Task started: Prodigal
[2024-01-24 13:01:09,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg685dcff5-4c79-4e83-aadb-f2316bc9fdad/GCF_007998985.1_ASM799898v1_genomic.fna.gz | prodigal -d GCF_007998985.1_ASM799898v1_genomic.fna/cds.fna -a GCF_007998985.1_ASM799898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:16,127] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:16,127] [INFO] Task started: HMMsearch
[2024-01-24 13:01:16,128] [INFO] Running command: hmmsearch --tblout GCF_007998985.1_ASM799898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11866d2d-2cee-48fd-9c50-d25fcff50014/dqc_reference/reference_markers.hmm GCF_007998985.1_ASM799898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:16,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:16,417] [INFO] Found 6/6 markers.
[2024-01-24 13:01:16,444] [INFO] Query marker FASTA was written to GCF_007998985.1_ASM799898v1_genomic.fna/markers.fasta
[2024-01-24 13:01:16,444] [INFO] Task started: Blastn
[2024-01-24 13:01:16,444] [INFO] Running command: blastn -query GCF_007998985.1_ASM799898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11866d2d-2cee-48fd-9c50-d25fcff50014/dqc_reference/reference_markers.fasta -out GCF_007998985.1_ASM799898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:17,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:17,339] [INFO] Selected 17 target genomes.
[2024-01-24 13:01:17,339] [INFO] Target genome list was writen to GCF_007998985.1_ASM799898v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:17,369] [INFO] Task started: fastANI
[2024-01-24 13:01:17,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg685dcff5-4c79-4e83-aadb-f2316bc9fdad/GCF_007998985.1_ASM799898v1_genomic.fna.gz --refList GCF_007998985.1_ASM799898v1_genomic.fna/target_genomes.txt --output GCF_007998985.1_ASM799898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:26,614] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:26,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11866d2d-2cee-48fd-9c50-d25fcff50014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:26,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11866d2d-2cee-48fd-9c50-d25fcff50014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:26,628] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:26,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:26,628] [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 xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	100.0	742	742	95	conclusive
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.8011	352	742	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.6599	415	742	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.1663	346	742	95	below_threshold
Sphingomonas edaphi	strain=DAC4	GCA_003583725.1	2315689	2315689	type	True	79.0096	368	742	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.5868	304	742	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.4214	312	742	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	78.3886	295	742	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	78.3382	298	742	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	78.2942	248	742	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.2181	227	742	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	78.1025	258	742	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	78.0937	260	742	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	77.8864	239	742	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.4835	194	742	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.2593	200	742	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.2374	203	742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:26,632] [INFO] DFAST Taxonomy check result was written to GCF_007998985.1_ASM799898v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:26,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:26,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:26,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11866d2d-2cee-48fd-9c50-d25fcff50014/dqc_reference/checkm_data
[2024-01-24 13:01:26,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:26,690] [INFO] Task started: CheckM
[2024-01-24 13:01:26,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007998985.1_ASM799898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007998985.1_ASM799898v1_genomic.fna/checkm_input GCF_007998985.1_ASM799898v1_genomic.fna/checkm_result
[2024-01-24 13:01:51,654] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:51,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:51,674] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:51,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:51,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007998985.1_ASM799898v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:51,675] [INFO] Task started: Blastn
[2024-01-24 13:01:51,675] [INFO] Running command: blastn -query GCF_007998985.1_ASM799898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11866d2d-2cee-48fd-9c50-d25fcff50014/dqc_reference/reference_markers_gtdb.fasta -out GCF_007998985.1_ASM799898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:53,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:53,251] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:53,251] [INFO] Target genome list was writen to GCF_007998985.1_ASM799898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:53,269] [INFO] Task started: fastANI
[2024-01-24 13:01:53,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg685dcff5-4c79-4e83-aadb-f2316bc9fdad/GCF_007998985.1_ASM799898v1_genomic.fna.gz --refList GCF_007998985.1_ASM799898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007998985.1_ASM799898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:00,924] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:00,938] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:00,938] [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_007998985.1	s__Sphingomicrobium xanthus	100.0	742	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014396585.1	s__Sphingomicrobium rhizophilum	79.7862	353	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	79.6599	415	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	79.2429	280	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	79.1403	348	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583725.1	s__Sphingomicrobium edaphi	79.0096	368	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.5776	304	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	78.447	310	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014195685.1	s__Sphingomicrobium lutaoense	78.2784	249	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924655.1	s__Sphingomicrobium sp016924655	78.1437	247	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873375.1	s__Sphingomicrobium sp014873375	78.1233	244	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.9822	241	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	77.897	193	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_014334115.1	s__Sphingomonas sp014334115	77.6061	192	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	77.4987	193	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361785.1	s__Sphingomicrobium sp013361785	77.4217	195	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:00,945] [INFO] GTDB search result was written to GCF_007998985.1_ASM799898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:00,946] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:00,950] [INFO] DFAST_QC result json was written to GCF_007998985.1_ASM799898v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:00,950] [INFO] DFAST_QC completed!
[2024-01-24 13:02:00,950] [INFO] Total running time: 0h0m53s