[2024-01-25 19:44:20,826] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:20,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:20,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b5c828a-213c-4c00-90e5-1f3ebb500ead/dqc_reference
[2024-01-25 19:44:21,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:21,977] [INFO] Task started: Prodigal
[2024-01-25 19:44:21,977] [INFO] Running command: gunzip -c /var/lib/cwl/stgad4908a6-0eaa-4757-a594-74c229152c02/GCF_013408095.1_ASM1340809v1_genomic.fna.gz | prodigal -d GCF_013408095.1_ASM1340809v1_genomic.fna/cds.fna -a GCF_013408095.1_ASM1340809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:31,240] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:31,240] [INFO] Task started: HMMsearch
[2024-01-25 19:44:31,240] [INFO] Running command: hmmsearch --tblout GCF_013408095.1_ASM1340809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b5c828a-213c-4c00-90e5-1f3ebb500ead/dqc_reference/reference_markers.hmm GCF_013408095.1_ASM1340809v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:31,445] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:31,446] [INFO] Found 6/6 markers.
[2024-01-25 19:44:31,477] [INFO] Query marker FASTA was written to GCF_013408095.1_ASM1340809v1_genomic.fna/markers.fasta
[2024-01-25 19:44:31,478] [INFO] Task started: Blastn
[2024-01-25 19:44:31,478] [INFO] Running command: blastn -query GCF_013408095.1_ASM1340809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b5c828a-213c-4c00-90e5-1f3ebb500ead/dqc_reference/reference_markers.fasta -out GCF_013408095.1_ASM1340809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:32,392] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:32,395] [INFO] Selected 23 target genomes.
[2024-01-25 19:44:32,395] [INFO] Target genome list was writen to GCF_013408095.1_ASM1340809v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:32,405] [INFO] Task started: fastANI
[2024-01-25 19:44:32,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4908a6-0eaa-4757-a594-74c229152c02/GCF_013408095.1_ASM1340809v1_genomic.fna.gz --refList GCF_013408095.1_ASM1340809v1_genomic.fna/target_genomes.txt --output GCF_013408095.1_ASM1340809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:49,593] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:49,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b5c828a-213c-4c00-90e5-1f3ebb500ead/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:49,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b5c828a-213c-4c00-90e5-1f3ebb500ead/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:49,607] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:44:49,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:49,608] [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
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	100.0	1185	1186	95	conclusive
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	99.9898	1182	1186	95	conclusive
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	80.4028	410	1186	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	80.0084	469	1186	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	79.3279	373	1186	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	79.296	453	1186	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	79.2698	420	1186	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	79.2534	456	1186	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.251	389	1186	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	79.2102	429	1186	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	79.1791	406	1186	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	79.0468	355	1186	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.9901	404	1186	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.8866	407	1186	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	78.8816	376	1186	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	78.8419	370	1186	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.8325	405	1186	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.8259	388	1186	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.5913	327	1186	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.3544	301	1186	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	78.1774	341	1186	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.1522	278	1186	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	78.1391	346	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:49,609] [INFO] DFAST Taxonomy check result was written to GCF_013408095.1_ASM1340809v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:49,609] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:49,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:49,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b5c828a-213c-4c00-90e5-1f3ebb500ead/dqc_reference/checkm_data
[2024-01-25 19:44:49,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:49,649] [INFO] Task started: CheckM
[2024-01-25 19:44:49,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408095.1_ASM1340809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408095.1_ASM1340809v1_genomic.fna/checkm_input GCF_013408095.1_ASM1340809v1_genomic.fna/checkm_result
[2024-01-25 19:45:18,967] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:18,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:19,002] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:19,002] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:19,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408095.1_ASM1340809v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:19,003] [INFO] Task started: Blastn
[2024-01-25 19:45:19,003] [INFO] Running command: blastn -query GCF_013408095.1_ASM1340809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b5c828a-213c-4c00-90e5-1f3ebb500ead/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408095.1_ASM1340809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:20,818] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:20,821] [INFO] Selected 24 target genomes.
[2024-01-25 19:45:20,821] [INFO] Target genome list was writen to GCF_013408095.1_ASM1340809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:20,846] [INFO] Task started: fastANI
[2024-01-25 19:45:20,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4908a6-0eaa-4757-a594-74c229152c02/GCF_013408095.1_ASM1340809v1_genomic.fna.gz --refList GCF_013408095.1_ASM1340809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408095.1_ASM1340809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:39,792] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:39,806] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:39,806] [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_013408095.1	s__Novosphingobium marinum	100.0	1185	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002556635.1	s__Novosphingobium sp002556635	81.3739	555	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	80.4028	410	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813245.1	s__Novosphingobium kunmingense	79.315	374	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	79.296	453	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_000802225.1	s__Novosphingobium malaysiense	79.2825	426	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015865035.1	s__Novosphingobium sp015865035	79.2465	422	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	79.2048	429	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640675.1	s__Novosphingobium endophyticum	79.1725	406	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	79.036	342	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	78.9881	405	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230305.1	s__Novosphingobium aerophilum	78.9523	370	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	-
GCF_005145025.1	s__Novosphingobium sp005145025	78.9449	363	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	78.9071	408	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	78.8409	384	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445125.1	s__Novosphingobium lindaniclasticum	78.838	370	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298105.1	s__Novosphingobium sp001298105	78.7661	376	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCA_001725355.1	s__Novosphingobium sp001725355	78.7496	323	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	78.6099	352	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	78.5857	328	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.3672	301	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176395.1	s__Novosphingobium sp900176395	78.2606	325	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830315.1	s__Novosphingobium taihuense	78.1599	346	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	78.1522	278	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:39,808] [INFO] GTDB search result was written to GCF_013408095.1_ASM1340809v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:39,808] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:39,812] [INFO] DFAST_QC result json was written to GCF_013408095.1_ASM1340809v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:39,812] [INFO] DFAST_QC completed!
[2024-01-25 19:45:39,812] [INFO] Total running time: 0h1m19s