[2023-06-29 16:46:55,459] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:46:55,461] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:46:55,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ee84a08-a497-486b-97ef-75d1a20caaaa/dqc_reference
[2023-06-29 16:46:56,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:46:56,832] [INFO] Task started: Prodigal
[2023-06-29 16:46:56,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg605bb8ac-4ce0-494d-9eba-e456eb453c6e/GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:47:10,151] [INFO] Task succeeded: Prodigal
[2023-06-29 16:47:10,151] [INFO] Task started: HMMsearch
[2023-06-29 16:47:10,151] [INFO] Running command: hmmsearch --tblout GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ee84a08-a497-486b-97ef-75d1a20caaaa/dqc_reference/reference_markers.hmm GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:47:10,446] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:47:10,449] [INFO] Found 6/6 markers.
[2023-06-29 16:47:10,485] [INFO] Query marker FASTA was written to GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:47:10,485] [INFO] Task started: Blastn
[2023-06-29 16:47:10,486] [INFO] Running command: blastn -query GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee84a08-a497-486b-97ef-75d1a20caaaa/dqc_reference/reference_markers.fasta -out GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:11,540] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:11,544] [INFO] Selected 22 target genomes.
[2023-06-29 16:47:11,544] [INFO] Target genome list was writen to GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:47:11,565] [INFO] Task started: fastANI
[2023-06-29 16:47:11,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg605bb8ac-4ce0-494d-9eba-e456eb453c6e/GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:47:28,091] [INFO] Task succeeded: fastANI
[2023-06-29 16:47:28,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ee84a08-a497-486b-97ef-75d1a20caaaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:47:28,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ee84a08-a497-486b-97ef-75d1a20caaaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:47:28,109] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:47:28,109] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:47:28,109] [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
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	79.194	445	1236	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	79.188	483	1236	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	79.0148	482	1236	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	78.8558	473	1236	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	78.7146	449	1236	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	78.5359	423	1236	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	78.4603	428	1236	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	78.4405	413	1236	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.4095	407	1236	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	78.3191	364	1236	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.1332	355	1236	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	78.0868	304	1236	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	78.0827	356	1236	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	77.959	316	1236	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	77.9024	292	1236	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.9021	316	1236	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.8931	381	1236	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	77.7802	318	1236	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.683	333	1236	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.6623	357	1236	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	77.3288	276	1236	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	77.3153	246	1236	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:47:28,111] [INFO] DFAST Taxonomy check result was written to GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:47:28,112] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:47:28,112] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:47:28,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ee84a08-a497-486b-97ef-75d1a20caaaa/dqc_reference/checkm_data
[2023-06-29 16:47:28,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:47:28,156] [INFO] Task started: CheckM
[2023-06-29 16:47:28,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:48:30,922] [INFO] Task succeeded: CheckM
[2023-06-29 16:48:30,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:48:30,942] [INFO] ===== Completeness check finished =====
[2023-06-29 16:48:30,942] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:48:30,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:48:30,943] [INFO] Task started: Blastn
[2023-06-29 16:48:30,943] [INFO] Running command: blastn -query GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee84a08-a497-486b-97ef-75d1a20caaaa/dqc_reference/reference_markers_gtdb.fasta -out GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:48:32,848] [INFO] Task succeeded: Blastn
[2023-06-29 16:48:32,853] [INFO] Selected 12 target genomes.
[2023-06-29 16:48:32,854] [INFO] Target genome list was writen to GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:48:32,860] [INFO] Task started: fastANI
[2023-06-29 16:48:32,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg605bb8ac-4ce0-494d-9eba-e456eb453c6e/GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:48:41,980] [INFO] Task succeeded: fastANI
[2023-06-29 16:48:41,993] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:48:41,993] [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_001899805.1	s__66-474 sp001899805	99.9886	1231	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	100.00	100.00	0.98	0.97	3	conclusive
GCA_018241365.1	s__66-474 sp018241365	84.6338	729	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971925.1	s__66-474 sp018971925	83.3597	474	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299705.1	s__66-474 sp004299705	83.2328	735	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241145.1	s__66-474 sp018241145	80.5776	471	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299555.1	s__66-474 sp004299555	80.0478	550	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	79.393	466	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842975.1	s__Rhodanobacter sp014842975	79.3827	474	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	79.3034	479	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_002001105.1	s__Rhodanobacter sp002001105	79.0971	516	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335105.1	s__Rhodanobacter denitrificans_A	78.951	475	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004143945.1	s__Dokdonella_A sp004143945	78.1226	359	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:48:41,996] [INFO] GTDB search result was written to GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:48:41,996] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:48:42,004] [INFO] DFAST_QC result json was written to GCA_937862995.1_SRR5626776_bin.13_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:48:42,004] [INFO] DFAST_QC completed!
[2023-06-29 16:48:42,004] [INFO] Total running time: 0h1m47s