[2024-01-24 15:19:50,255] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:50,257] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:50,257] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e0e4a78-92ad-4c83-974d-9fbdf5126933/dqc_reference
[2024-01-24 15:19:51,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:51,585] [INFO] Task started: Prodigal
[2024-01-24 15:19:51,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b2942d9-0d25-4466-93a1-71f07f687a09/GCF_003367235.1_ASM336723v1_genomic.fna.gz | prodigal -d GCF_003367235.1_ASM336723v1_genomic.fna/cds.fna -a GCF_003367235.1_ASM336723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:02,356] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:02,356] [INFO] Task started: HMMsearch
[2024-01-24 15:20:02,357] [INFO] Running command: hmmsearch --tblout GCF_003367235.1_ASM336723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e0e4a78-92ad-4c83-974d-9fbdf5126933/dqc_reference/reference_markers.hmm GCF_003367235.1_ASM336723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:02,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:02,634] [INFO] Found 6/6 markers.
[2024-01-24 15:20:02,675] [INFO] Query marker FASTA was written to GCF_003367235.1_ASM336723v1_genomic.fna/markers.fasta
[2024-01-24 15:20:02,675] [INFO] Task started: Blastn
[2024-01-24 15:20:02,675] [INFO] Running command: blastn -query GCF_003367235.1_ASM336723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e0e4a78-92ad-4c83-974d-9fbdf5126933/dqc_reference/reference_markers.fasta -out GCF_003367235.1_ASM336723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:03,512] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:03,517] [INFO] Selected 25 target genomes.
[2024-01-24 15:20:03,518] [INFO] Target genome list was writen to GCF_003367235.1_ASM336723v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:03,533] [INFO] Task started: fastANI
[2024-01-24 15:20:03,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2942d9-0d25-4466-93a1-71f07f687a09/GCF_003367235.1_ASM336723v1_genomic.fna.gz --refList GCF_003367235.1_ASM336723v1_genomic.fna/target_genomes.txt --output GCF_003367235.1_ASM336723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:19,897] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:19,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e0e4a78-92ad-4c83-974d-9fbdf5126933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:19,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e0e4a78-92ad-4c83-974d-9fbdf5126933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:19,923] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:19,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:19,924] [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
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	100.0	1070	1070	95	conclusive
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	78.4368	292	1070	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	77.8666	269	1070	95	below_threshold
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	77.7095	255	1070	95	below_threshold
Sphingorhabdus rigui	strain=DSM 29050	GCA_014196595.1	1282858	1282858	type	True	77.572	220	1070	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	77.5495	232	1070	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	77.5059	205	1070	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	77.4905	208	1070	95	below_threshold
Sphingobium vermicomposti	strain=DSM 21299	GCA_011762025.1	529005	529005	type	True	77.3937	156	1070	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.3794	174	1070	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.36	152	1070	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	77.2584	175	1070	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.2582	209	1070	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.2411	182	1070	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.2355	232	1070	95	below_threshold
Sphingorhabdus wooponensis	strain=03SU3-P	GCA_003933235.1	940136	940136	type	True	77.2236	170	1070	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.139	151	1070	95	below_threshold
Sphingomonas parapaucimobilis	strain=NBRC 15100	GCA_000787715.1	28213	28213	type	True	77.1106	159	1070	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	77.1101	177	1070	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	77.0825	164	1070	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	77.0504	158	1070	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	77.0467	166	1070	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	76.5679	85	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:19,929] [INFO] DFAST Taxonomy check result was written to GCF_003367235.1_ASM336723v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:19,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:19,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:19,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e0e4a78-92ad-4c83-974d-9fbdf5126933/dqc_reference/checkm_data
[2024-01-24 15:20:19,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:19,969] [INFO] Task started: CheckM
[2024-01-24 15:20:19,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367235.1_ASM336723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367235.1_ASM336723v1_genomic.fna/checkm_input GCF_003367235.1_ASM336723v1_genomic.fna/checkm_result
[2024-01-24 15:20:54,636] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:54,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:54,659] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:54,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:54,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367235.1_ASM336723v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:54,661] [INFO] Task started: Blastn
[2024-01-24 15:20:54,661] [INFO] Running command: blastn -query GCF_003367235.1_ASM336723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e0e4a78-92ad-4c83-974d-9fbdf5126933/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367235.1_ASM336723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:56,179] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:56,183] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:56,184] [INFO] Target genome list was writen to GCF_003367235.1_ASM336723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:56,246] [INFO] Task started: fastANI
[2024-01-24 15:20:56,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2942d9-0d25-4466-93a1-71f07f687a09/GCF_003367235.1_ASM336723v1_genomic.fna.gz --refList GCF_003367235.1_ASM336723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367235.1_ASM336723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:03,673] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:03,691] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:03,692] [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_003367235.1	s__Sphingorhabdus_B sp003367235	100.0	1070	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016707885.1	s__Sphingorhabdus_B sp016707885	89.6551	830	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987825.1	s__Sphingorhabdus_B sp017987825	84.0767	457	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720115.1	s__Sphingorhabdus_B sp016720115	82.8391	655	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.85	99.81	0.95	0.95	3	-
GCA_016721875.1	s__Sphingorhabdus_B sp016721875	79.4301	426	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.47	99.39	0.95	0.94	3	-
GCA_005518185.1	s__Chakrabartia godavariana	77.6676	213	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297725.1	s__Sphingorhabdus_B sp013297725	77.4338	291	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	77.1106	159	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCF_011047315.1	s__Erythrobacter sp011047315	77.0855	181	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	76.6754	149	1070	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 15:21:03,694] [INFO] GTDB search result was written to GCF_003367235.1_ASM336723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:03,694] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:03,700] [INFO] DFAST_QC result json was written to GCF_003367235.1_ASM336723v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:03,700] [INFO] DFAST_QC completed!
[2024-01-24 15:21:03,700] [INFO] Total running time: 0h1m13s