[2023-06-19 08:43:01,007] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:43:01,010] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:43:01,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg134b8cb0-801a-40b1-be70-41eb1fb99452/dqc_reference
[2023-06-19 08:43:02,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:43:02,244] [INFO] Task started: Prodigal
[2023-06-19 08:43:02,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg81c1b005-7808-469d-86c2-1c23a3b750c5/GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:43:23,576] [INFO] Task succeeded: Prodigal
[2023-06-19 08:43:23,576] [INFO] Task started: HMMsearch
[2023-06-19 08:43:23,577] [INFO] Running command: hmmsearch --tblout GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg134b8cb0-801a-40b1-be70-41eb1fb99452/dqc_reference/reference_markers.hmm GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:43:23,904] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:43:23,906] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg81c1b005-7808-469d-86c2-1c23a3b750c5/GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-19 08:43:23,958] [INFO] Query marker FASTA was written to GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 08:43:23,959] [INFO] Task started: Blastn
[2023-06-19 08:43:23,959] [INFO] Running command: blastn -query GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg134b8cb0-801a-40b1-be70-41eb1fb99452/dqc_reference/reference_markers.fasta -out GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:43:24,907] [INFO] Task succeeded: Blastn
[2023-06-19 08:43:24,913] [INFO] Selected 15 target genomes.
[2023-06-19 08:43:24,913] [INFO] Target genome list was writen to GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 08:43:24,916] [INFO] Task started: fastANI
[2023-06-19 08:43:24,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c1b005-7808-469d-86c2-1c23a3b750c5/GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:43:43,163] [INFO] Task succeeded: fastANI
[2023-06-19 08:43:43,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg134b8cb0-801a-40b1-be70-41eb1fb99452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:43:43,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg134b8cb0-801a-40b1-be70-41eb1fb99452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:43:43,176] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-06-19 08:43:43,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 08:43:43,177] [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
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	95.5278	1737	1962	95	conclusive
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	95.4427	1761	1962	95	conclusive
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	84.1696	1057	1962	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	84.0957	911	1962	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	82.0029	952	1962	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	81.8213	751	1962	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.8141	883	1962	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	81.5481	865	1962	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.7071	879	1962	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	80.6037	821	1962	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	80.3285	788	1962	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	80.2017	762	1962	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.1816	764	1962	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.663	652	1962	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.4933	546	1962	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:43:43,180] [INFO] DFAST Taxonomy check result was written to GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 08:43:43,181] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:43:43,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:43:43,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg134b8cb0-801a-40b1-be70-41eb1fb99452/dqc_reference/checkm_data
[2023-06-19 08:43:43,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:43:43,245] [INFO] Task started: CheckM
[2023-06-19 08:43:43,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 08:45:10,061] [INFO] Task succeeded: CheckM
[2023-06-19 08:45:10,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:45:10,088] [INFO] ===== Completeness check finished =====
[2023-06-19 08:45:10,088] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:45:10,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 08:45:10,089] [INFO] Task started: Blastn
[2023-06-19 08:45:10,089] [INFO] Running command: blastn -query GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg134b8cb0-801a-40b1-be70-41eb1fb99452/dqc_reference/reference_markers_gtdb.fasta -out GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:45:11,779] [INFO] Task succeeded: Blastn
[2023-06-19 08:45:11,789] [INFO] Selected 13 target genomes.
[2023-06-19 08:45:11,789] [INFO] Target genome list was writen to GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:45:11,797] [INFO] Task started: fastANI
[2023-06-19 08:45:11,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c1b005-7808-469d-86c2-1c23a3b750c5/GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:45:27,534] [INFO] Task succeeded: fastANI
[2023-06-19 08:45:27,551] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-19 08:45:27,551] [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_001571325.1	s__Comamonas tsuruhatensis	98.4084	1746	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	inconclusive
GCF_001598795.1	s__Comamonas acidovorans	95.5158	1738	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	97.72	96.19	0.89	0.80	41	inconclusive
GCF_001544075.1	s__Comamonas terrae	84.2023	1054	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637085.1	s__Comamonas phosphati	84.0772	913	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236485.1	s__Comamonas sp019236485	82.9914	704	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429845.1	s__Comamonas composti	82.6061	922	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761245.1	s__Comamonas testosteroni_C	82.0703	942	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.84	98.53	0.90	0.90	4	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	81.8137	763	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCF_000400995.2	s__MR-S7 sp000400995	81.7271	871	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_014204315.1	s__Comamonas konjaci_A	81.572	878	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900461435.1	s__Comamonas terrigena	81.4792	874	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCF_900564145.1	s__Comamonas sp900564145	81.4349	892	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428875.1	s__Xylophilus sp016428875	80.4168	731	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:45:27,554] [INFO] GTDB search result was written to GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 08:45:27,554] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:45:27,560] [INFO] DFAST_QC result json was written to GCA_937997005.1_SRR3901707_bin.56_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 08:45:27,560] [INFO] DFAST_QC completed!
[2023-06-19 08:45:27,560] [INFO] Total running time: 0h2m27s