[2023-06-13 23:19:05,214] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:19:05,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:19:05,217] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9feb450-e804-476d-acce-27d4e5ca4763/dqc_reference
[2023-06-13 23:19:06,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:19:06,437] [INFO] Task started: Prodigal
[2023-06-13 23:19:06,437] [INFO] Running command: gunzip -c /var/lib/cwl/stg384bc1ea-91c4-4948-9e19-fde594f740a5/GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:19:14,155] [INFO] Task succeeded: Prodigal
[2023-06-13 23:19:14,156] [INFO] Task started: HMMsearch
[2023-06-13 23:19:14,156] [INFO] Running command: hmmsearch --tblout GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9feb450-e804-476d-acce-27d4e5ca4763/dqc_reference/reference_markers.hmm GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:19:14,420] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:19:14,422] [INFO] Found 6/6 markers.
[2023-06-13 23:19:14,452] [INFO] Query marker FASTA was written to GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 23:19:14,452] [INFO] Task started: Blastn
[2023-06-13 23:19:14,453] [INFO] Running command: blastn -query GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9feb450-e804-476d-acce-27d4e5ca4763/dqc_reference/reference_markers.fasta -out GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:19:15,437] [INFO] Task succeeded: Blastn
[2023-06-13 23:19:15,441] [INFO] Selected 24 target genomes.
[2023-06-13 23:19:15,442] [INFO] Target genome list was writen to GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 23:19:15,447] [INFO] Task started: fastANI
[2023-06-13 23:19:15,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg384bc1ea-91c4-4948-9e19-fde594f740a5/GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:19:30,742] [INFO] Task succeeded: fastANI
[2023-06-13 23:19:30,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9feb450-e804-476d-acce-27d4e5ca4763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:19:30,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9feb450-e804-476d-acce-27d4e5ca4763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:19:30,768] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:19:30,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 23:19:30,768] [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
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	81.7657	489	751	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.4124	458	751	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	81.3708	439	751	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	81.3538	503	751	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.2114	468	751	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	81.1958	450	751	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.1302	467	751	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	81.0447	466	751	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	80.8778	478	751	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	80.7307	423	751	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.6385	417	751	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	80.5518	418	751	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.4444	356	751	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.414	464	751	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	80.3429	383	751	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.3423	459	751	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.2931	365	751	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	80.1785	352	751	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	80.036	408	751	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	80.0314	389	751	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	79.9168	420	751	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	79.8889	409	751	95	below_threshold
Lysobacter oculi	strain=83-4	GCA_003293695.1	2698682	2698682	type	True	79.5497	335	751	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	79.3929	382	751	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 23:19:30,770] [INFO] DFAST Taxonomy check result was written to GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 23:19:30,771] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:19:30,771] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:19:30,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9feb450-e804-476d-acce-27d4e5ca4763/dqc_reference/checkm_data
[2023-06-13 23:19:30,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:19:30,811] [INFO] Task started: CheckM
[2023-06-13 23:19:30,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 23:20:01,239] [INFO] Task succeeded: CheckM
[2023-06-13 23:20:01,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.89%
Strain heterogeneity: 12.50%
--------------------------------------------------------------------------------
[2023-06-13 23:20:01,269] [INFO] ===== Completeness check finished =====
[2023-06-13 23:20:01,270] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:20:01,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 23:20:01,270] [INFO] Task started: Blastn
[2023-06-13 23:20:01,271] [INFO] Running command: blastn -query GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9feb450-e804-476d-acce-27d4e5ca4763/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:20:03,152] [INFO] Task succeeded: Blastn
[2023-06-13 23:20:03,157] [INFO] Selected 18 target genomes.
[2023-06-13 23:20:03,157] [INFO] Target genome list was writen to GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:20:03,227] [INFO] Task started: fastANI
[2023-06-13 23:20:03,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg384bc1ea-91c4-4948-9e19-fde594f740a5/GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:20:15,057] [INFO] Task succeeded: fastANI
[2023-06-13 23:20:15,079] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 23:20:15,079] [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
GCA_019115725.1	s__Luteimonas excrementigallinarum	98.0977	543	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001717465.1	s__Luteimonas sp001717465	84.0512	581	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	81.7655	489	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	81.397	459	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425525.1	s__Luteimonas sp013425525	81.3812	501	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312895.1	s__Luteimonas sp008312895	81.2729	482	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	81.2403	466	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	81.2353	447	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014836665.1	s__Luteimonas sp014836665	81.1299	467	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	81.0697	441	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_007859305.1	s__Luteimonas wenzhouensis	81.0583	465	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_007859325.1	s__Luteimonas marina	80.8991	476	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	80.8749	421	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	80.8015	417	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_008244685.1	s__Luteimonas sp008244685	80.4171	464	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	80.3839	429	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014645.1	s__Luteimonas sp001014645	80.2149	450	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830115.1	s__Lysobacter ruishenii	80.0314	389	751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 23:20:15,085] [INFO] GTDB search result was written to GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 23:20:15,086] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:20:15,093] [INFO] DFAST_QC result json was written to GCA_938014845.1_SRR6713635_bin.64_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 23:20:15,094] [INFO] DFAST_QC completed!
[2023-06-13 23:20:15,094] [INFO] Total running time: 0h1m10s