[2024-01-24 13:58:26,160] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:26,161] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:26,161] [INFO] DQC Reference Directory: /var/lib/cwl/stge32e7e24-8bd3-4c99-ae68-e3bda8ee85cf/dqc_reference
[2024-01-24 13:58:27,469] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:27,470] [INFO] Task started: Prodigal
[2024-01-24 13:58:27,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg49c71d85-5379-4980-8797-93cbd0e09cef/GCF_014640055.1_ASM1464005v1_genomic.fna.gz | prodigal -d GCF_014640055.1_ASM1464005v1_genomic.fna/cds.fna -a GCF_014640055.1_ASM1464005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:37,881] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:37,882] [INFO] Task started: HMMsearch
[2024-01-24 13:58:37,882] [INFO] Running command: hmmsearch --tblout GCF_014640055.1_ASM1464005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge32e7e24-8bd3-4c99-ae68-e3bda8ee85cf/dqc_reference/reference_markers.hmm GCF_014640055.1_ASM1464005v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:38,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:38,173] [INFO] Found 6/6 markers.
[2024-01-24 13:58:38,208] [INFO] Query marker FASTA was written to GCF_014640055.1_ASM1464005v1_genomic.fna/markers.fasta
[2024-01-24 13:58:38,209] [INFO] Task started: Blastn
[2024-01-24 13:58:38,209] [INFO] Running command: blastn -query GCF_014640055.1_ASM1464005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge32e7e24-8bd3-4c99-ae68-e3bda8ee85cf/dqc_reference/reference_markers.fasta -out GCF_014640055.1_ASM1464005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:39,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:39,250] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:39,251] [INFO] Target genome list was writen to GCF_014640055.1_ASM1464005v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:39,262] [INFO] Task started: fastANI
[2024-01-24 13:58:39,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg49c71d85-5379-4980-8797-93cbd0e09cef/GCF_014640055.1_ASM1464005v1_genomic.fna.gz --refList GCF_014640055.1_ASM1464005v1_genomic.fna/target_genomes.txt --output GCF_014640055.1_ASM1464005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:56,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:56,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge32e7e24-8bd3-4c99-ae68-e3bda8ee85cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:56,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge32e7e24-8bd3-4c99-ae68-e3bda8ee85cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:56,748] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:56,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:56,749] [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=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	100.0	1183	1184	95	conclusive
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	99.9956	1176	1184	95	conclusive
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	80.4855	409	1184	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	80.0272	474	1184	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	79.3863	452	1184	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	79.2998	369	1184	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	79.285	454	1184	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.2734	394	1184	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	79.2395	427	1184	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	79.1736	430	1184	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	79.1605	407	1184	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	79.0976	397	1184	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	79.0584	357	1184	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	79.0299	394	1184	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.8555	388	1184	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.8122	406	1184	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	78.743	387	1184	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	78.7361	377	1184	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.6545	331	1184	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.4513	289	1184	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	78.3351	347	1184	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	78.2655	343	1184	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.1305	272	1184	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,750] [INFO] DFAST Taxonomy check result was written to GCF_014640055.1_ASM1464005v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:56,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:56,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:56,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge32e7e24-8bd3-4c99-ae68-e3bda8ee85cf/dqc_reference/checkm_data
[2024-01-24 13:58:56,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:56,787] [INFO] Task started: CheckM
[2024-01-24 13:58:56,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640055.1_ASM1464005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640055.1_ASM1464005v1_genomic.fna/checkm_input GCF_014640055.1_ASM1464005v1_genomic.fna/checkm_result
[2024-01-24 13:59:29,447] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:29,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:29,471] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:29,471] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:29,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640055.1_ASM1464005v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:29,472] [INFO] Task started: Blastn
[2024-01-24 13:59:29,472] [INFO] Running command: blastn -query GCF_014640055.1_ASM1464005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge32e7e24-8bd3-4c99-ae68-e3bda8ee85cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640055.1_ASM1464005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:31,280] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:31,284] [INFO] Selected 24 target genomes.
[2024-01-24 13:59:31,285] [INFO] Target genome list was writen to GCF_014640055.1_ASM1464005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:31,315] [INFO] Task started: fastANI
[2024-01-24 13:59:31,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg49c71d85-5379-4980-8797-93cbd0e09cef/GCF_014640055.1_ASM1464005v1_genomic.fna.gz --refList GCF_014640055.1_ASM1464005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640055.1_ASM1464005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:49,240] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:49,266] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:49,267] [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	99.9956	1176	1184	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	81.3518	544	1184	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	80.4622	411	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	79.4061	453	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_002813245.1	s__Novosphingobium kunmingense	79.2939	370	1184	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	79.2394	427	1184	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	79.1736	430	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802225.1	s__Novosphingobium malaysiense	79.1523	439	1184	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	79.1434	409	1184	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	79.0607	396	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145025.1	s__Novosphingobium sp005145025	79.0483	355	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	79.0299	394	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725355.1	s__Novosphingobium sp001725355	78.9951	319	1184	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	78.876	381	1184	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	78.8687	356	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230305.1	s__Novosphingobium aerophilum	78.8449	376	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	-
GCF_000445125.1	s__Novosphingobium lindaniclasticum	78.7514	376	1184	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	78.7204	382	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	78.6611	331	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	78.5342	358	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015529805.1	s__Qipengyuania soli	78.4508	290	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830315.1	s__Novosphingobium taihuense	78.2705	345	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900176395.1	s__Novosphingobium sp900176395	78.1723	332	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	78.1305	272	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:49,268] [INFO] GTDB search result was written to GCF_014640055.1_ASM1464005v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:49,269] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:49,274] [INFO] DFAST_QC result json was written to GCF_014640055.1_ASM1464005v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:49,275] [INFO] DFAST_QC completed!
[2024-01-24 13:59:49,275] [INFO] Total running time: 0h1m23s