[2023-06-18 17:52:57,197] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:52:57,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:52:57,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg6168d8e9-039c-4ed7-ae84-77d88b9bd0cf/dqc_reference
[2023-06-18 17:52:58,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:52:58,424] [INFO] Task started: Prodigal
[2023-06-18 17:52:58,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg20ec8053-7309-410d-a385-4213c7cb9e84/GCA_018241425.1_ASM1824142v1_genomic.fna.gz | prodigal -d GCA_018241425.1_ASM1824142v1_genomic.fna/cds.fna -a GCA_018241425.1_ASM1824142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:53:11,257] [INFO] Task succeeded: Prodigal
[2023-06-18 17:53:11,258] [INFO] Task started: HMMsearch
[2023-06-18 17:53:11,258] [INFO] Running command: hmmsearch --tblout GCA_018241425.1_ASM1824142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6168d8e9-039c-4ed7-ae84-77d88b9bd0cf/dqc_reference/reference_markers.hmm GCA_018241425.1_ASM1824142v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:53:11,525] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:53:11,527] [INFO] Found 6/6 markers.
[2023-06-18 17:53:11,590] [INFO] Query marker FASTA was written to GCA_018241425.1_ASM1824142v1_genomic.fna/markers.fasta
[2023-06-18 17:53:11,590] [INFO] Task started: Blastn
[2023-06-18 17:53:11,591] [INFO] Running command: blastn -query GCA_018241425.1_ASM1824142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6168d8e9-039c-4ed7-ae84-77d88b9bd0cf/dqc_reference/reference_markers.fasta -out GCA_018241425.1_ASM1824142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:53:12,460] [INFO] Task succeeded: Blastn
[2023-06-18 17:53:12,468] [INFO] Selected 31 target genomes.
[2023-06-18 17:53:12,469] [INFO] Target genome list was writen to GCA_018241425.1_ASM1824142v1_genomic.fna/target_genomes.txt
[2023-06-18 17:53:12,472] [INFO] Task started: fastANI
[2023-06-18 17:53:12,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ec8053-7309-410d-a385-4213c7cb9e84/GCA_018241425.1_ASM1824142v1_genomic.fna.gz --refList GCA_018241425.1_ASM1824142v1_genomic.fna/target_genomes.txt --output GCA_018241425.1_ASM1824142v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:53:32,752] [INFO] Task succeeded: fastANI
[2023-06-18 17:53:32,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6168d8e9-039c-4ed7-ae84-77d88b9bd0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:53:32,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6168d8e9-039c-4ed7-ae84-77d88b9bd0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:53:32,781] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:53:32,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:53:32,782] [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
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.0344	133	1454	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	76.991	195	1454	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.9311	192	1454	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	76.8963	151	1454	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.8935	225	1454	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.8879	201	1454	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.8704	195	1454	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.8182	217	1454	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.8158	193	1454	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.7472	198	1454	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.713	178	1454	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.6931	207	1454	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.6901	208	1454	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	76.6533	177	1454	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.6417	172	1454	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	76.6186	224	1454	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.6006	230	1454	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	76.5781	240	1454	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.5662	198	1454	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	76.5242	173	1454	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4367	174	1454	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	76.4186	169	1454	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.3542	96	1454	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.3453	145	1454	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	76.3429	141	1454	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.3195	203	1454	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3009	301	1454	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.2905	169	1454	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.2778	141	1454	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.0276	203	1454	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	75.9246	136	1454	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:53:32,784] [INFO] DFAST Taxonomy check result was written to GCA_018241425.1_ASM1824142v1_genomic.fna/tc_result.tsv
[2023-06-18 17:53:32,784] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:53:32,784] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:53:32,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6168d8e9-039c-4ed7-ae84-77d88b9bd0cf/dqc_reference/checkm_data
[2023-06-18 17:53:32,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:53:32,831] [INFO] Task started: CheckM
[2023-06-18 17:53:32,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018241425.1_ASM1824142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018241425.1_ASM1824142v1_genomic.fna/checkm_input GCA_018241425.1_ASM1824142v1_genomic.fna/checkm_result
[2023-06-18 17:54:12,589] [INFO] Task succeeded: CheckM
[2023-06-18 17:54:12,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:54:12,624] [INFO] ===== Completeness check finished =====
[2023-06-18 17:54:12,625] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:54:12,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018241425.1_ASM1824142v1_genomic.fna/markers.fasta)
[2023-06-18 17:54:12,625] [INFO] Task started: Blastn
[2023-06-18 17:54:12,626] [INFO] Running command: blastn -query GCA_018241425.1_ASM1824142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6168d8e9-039c-4ed7-ae84-77d88b9bd0cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_018241425.1_ASM1824142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:54:14,138] [INFO] Task succeeded: Blastn
[2023-06-18 17:54:14,147] [INFO] Selected 14 target genomes.
[2023-06-18 17:54:14,147] [INFO] Target genome list was writen to GCA_018241425.1_ASM1824142v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:54:14,156] [INFO] Task started: fastANI
[2023-06-18 17:54:14,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ec8053-7309-410d-a385-4213c7cb9e84/GCA_018241425.1_ASM1824142v1_genomic.fna.gz --refList GCA_018241425.1_ASM1824142v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018241425.1_ASM1824142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:54:23,648] [INFO] Task succeeded: fastANI
[2023-06-18 17:54:23,664] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:54:23,665] [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_018241425.1	s__13-2-20CM-66-19 sp018241425	100.0	1451	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018240525.1	s__13-2-20CM-66-19 sp018240525	81.5496	763	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005878835.1	s__13-2-20CM-66-19 sp005878835	80.3726	599	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.03	96.96	0.89	0.85	6	-
GCA_005878095.1	s__13-2-20CM-66-19 sp005878095	80.2883	550	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	99.52	99.52	0.84	0.84	2	-
GCA_005877965.1	s__13-2-20CM-66-19 sp005877965	80.2297	428	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247195.1	s__13-2-20CM-66-19 sp019247195	80.2004	555	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	99.26	99.26	0.88	0.88	2	-
GCA_001914695.1	s__13-2-20CM-66-19 sp001914695	80.042	523	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.00	96.94	0.81	0.73	19	-
GCA_018241445.1	s__13-2-20CM-66-19 sp018241445	79.9097	580	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242385.1	s__13-2-20CM-66-19 sp019242385	79.6948	327	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136935.1	s__13-2-20CM-66-19 sp003136935	79.4286	483	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	96.25	96.25	0.78	0.78	2	-
GCA_003242685.1	s__ZC4RG24 sp003242685	78.8884	374	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003156695.1	s__13-2-20CM-66-19 sp003156695	78.8856	370	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187495.1	s__CADEFQ01 sp019187495	78.1115	313	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002995625.1	s__UDEA-SF1 sp002995625	77.0465	162	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UDEA-SF1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:54:23,667] [INFO] GTDB search result was written to GCA_018241425.1_ASM1824142v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:54:23,667] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:54:23,673] [INFO] DFAST_QC result json was written to GCA_018241425.1_ASM1824142v1_genomic.fna/dqc_result.json
[2023-06-18 17:54:23,673] [INFO] DFAST_QC completed!
[2023-06-18 17:54:23,673] [INFO] Total running time: 0h1m26s