[2023-06-28 22:24:34,211] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:24:34,213] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:24:34,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd107ac4-f357-4b89-8eed-ca92d96ca629/dqc_reference
[2023-06-28 22:24:35,763] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:24:35,764] [INFO] Task started: Prodigal
[2023-06-28 22:24:35,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ff48d6c-e7ca-4325-95b5-216f33279999/GCA_020853405.1_ASM2085340v1_genomic.fna.gz | prodigal -d GCA_020853405.1_ASM2085340v1_genomic.fna/cds.fna -a GCA_020853405.1_ASM2085340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:24:44,817] [INFO] Task succeeded: Prodigal
[2023-06-28 22:24:44,818] [INFO] Task started: HMMsearch
[2023-06-28 22:24:44,818] [INFO] Running command: hmmsearch --tblout GCA_020853405.1_ASM2085340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd107ac4-f357-4b89-8eed-ca92d96ca629/dqc_reference/reference_markers.hmm GCA_020853405.1_ASM2085340v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:24:45,065] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:24:45,067] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ff48d6c-e7ca-4325-95b5-216f33279999/GCA_020853405.1_ASM2085340v1_genomic.fna.gz]
[2023-06-28 22:24:45,107] [INFO] Query marker FASTA was written to GCA_020853405.1_ASM2085340v1_genomic.fna/markers.fasta
[2023-06-28 22:24:45,108] [INFO] Task started: Blastn
[2023-06-28 22:24:45,108] [INFO] Running command: blastn -query GCA_020853405.1_ASM2085340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd107ac4-f357-4b89-8eed-ca92d96ca629/dqc_reference/reference_markers.fasta -out GCA_020853405.1_ASM2085340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:24:46,129] [INFO] Task succeeded: Blastn
[2023-06-28 22:24:46,133] [INFO] Selected 29 target genomes.
[2023-06-28 22:24:46,133] [INFO] Target genome list was writen to GCA_020853405.1_ASM2085340v1_genomic.fna/target_genomes.txt
[2023-06-28 22:24:46,135] [INFO] Task started: fastANI
[2023-06-28 22:24:46,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff48d6c-e7ca-4325-95b5-216f33279999/GCA_020853405.1_ASM2085340v1_genomic.fna.gz --refList GCA_020853405.1_ASM2085340v1_genomic.fna/target_genomes.txt --output GCA_020853405.1_ASM2085340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:25:08,433] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:08,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd107ac4-f357-4b89-8eed-ca92d96ca629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:25:08,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd107ac4-f357-4b89-8eed-ca92d96ca629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:25:08,460] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:25:08,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:25:08,460] [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
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	77.7512	299	973	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.6567	360	973	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.5548	395	973	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.5498	351	973	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.5057	359	973	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	77.4602	277	973	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	77.4573	277	973	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.2872	351	973	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	77.2005	306	973	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.1603	209	973	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.1357	379	973	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	77.0752	207	973	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.0621	287	973	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	77.0394	298	973	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	77.0171	296	973	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	76.8409	159	973	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	76.7447	308	973	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	76.5306	275	973	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.4329	172	973	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.4029	253	973	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.059	181	973	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	75.6997	141	973	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	75.632	173	973	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.5634	106	973	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	75.3664	104	973	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	75.2738	50	973	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	75.0734	51	973	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	74.9391	59	973	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:25:08,462] [INFO] DFAST Taxonomy check result was written to GCA_020853405.1_ASM2085340v1_genomic.fna/tc_result.tsv
[2023-06-28 22:25:08,463] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:25:08,463] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:25:08,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd107ac4-f357-4b89-8eed-ca92d96ca629/dqc_reference/checkm_data
[2023-06-28 22:25:08,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:25:08,502] [INFO] Task started: CheckM
[2023-06-28 22:25:08,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020853405.1_ASM2085340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020853405.1_ASM2085340v1_genomic.fna/checkm_input GCA_020853405.1_ASM2085340v1_genomic.fna/checkm_result
[2023-06-28 22:25:41,075] [INFO] Task succeeded: CheckM
[2023-06-28 22:25:41,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 12.50%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-28 22:25:41,102] [INFO] ===== Completeness check finished =====
[2023-06-28 22:25:41,103] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:25:41,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020853405.1_ASM2085340v1_genomic.fna/markers.fasta)
[2023-06-28 22:25:41,104] [INFO] Task started: Blastn
[2023-06-28 22:25:41,104] [INFO] Running command: blastn -query GCA_020853405.1_ASM2085340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd107ac4-f357-4b89-8eed-ca92d96ca629/dqc_reference/reference_markers_gtdb.fasta -out GCA_020853405.1_ASM2085340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:43,048] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:43,053] [INFO] Selected 33 target genomes.
[2023-06-28 22:25:43,054] [INFO] Target genome list was writen to GCA_020853405.1_ASM2085340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:25:43,080] [INFO] Task started: fastANI
[2023-06-28 22:25:43,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff48d6c-e7ca-4325-95b5-216f33279999/GCA_020853405.1_ASM2085340v1_genomic.fna.gz --refList GCA_020853405.1_ASM2085340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020853405.1_ASM2085340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:26:08,398] [INFO] Task succeeded: fastANI
[2023-06-28 22:26:08,425] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:26:08,425] [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_006704265.1	s__Elioraea sp006704265	78.5685	408	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	77.966	425	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	77.7322	351	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCA_007129145.1	s__Roseococcus sp007129145	77.6824	184	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	77.6726	425	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	77.5311	357	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	77.4718	363	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	77.4578	327	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	77.4275	408	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	77.4102	288	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129085.1	s__Roseomonas_C hellenica	77.3973	378	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	97.71	97.71	0.92	0.92	2	-
GCA_001898425.1	s__69-11 sp001898425	77.3825	315	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCF_009829925.1	s__Roseomonas coralli	77.3656	346	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464375.1	s__Roseomonas_B sp001464375	77.3148	347	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	77.3142	274	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_001941945.1	s__Roseomonas gilardii	77.2785	295	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	-
GCF_003116135.1	s__Roseomonas aestuarii	77.2525	393	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	77.2103	346	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307285.1	s__JAFKFI01 sp017307285	77.206	250	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307335.1	s__JAFKFJ01 sp017307335	77.1406	269	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982615.1	s__Roseomonas deserti	77.0955	383	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802185.1	s__Belnapia sp000802185	76.9674	338	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174305.1	s__Gluconacetobacter johannae	76.7374	143	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928045.1	s__CAIYPH01 sp903928045	76.5396	202	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	98.55	98.55	0.76	0.76	2	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	76.534	151	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCA_903845065.1	s__CAIYPH01 sp903845065	76.329	272	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	75.681	215	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	75.6578	169	973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCA_016789885.1	s__SHZI01 sp016789885	75.312	88	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242275.1	s__ZC4RG30 sp003242275	75.2695	108	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241525.1	s__SZAS-83 sp018241525	75.1903	176	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789845.1	s__SHZI01 sp016789845	75.1324	56	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:26:08,427] [INFO] GTDB search result was written to GCA_020853405.1_ASM2085340v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:26:08,428] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:26:08,434] [INFO] DFAST_QC result json was written to GCA_020853405.1_ASM2085340v1_genomic.fna/dqc_result.json
[2023-06-28 22:26:08,434] [INFO] DFAST_QC completed!
[2023-06-28 22:26:08,434] [INFO] Total running time: 0h1m34s