[2023-06-29 07:30:11,565] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:30:11,566] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:30:11,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d957d6c-0451-4115-bb8a-a21c6a16d467/dqc_reference
[2023-06-29 07:30:12,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:30:12,749] [INFO] Task started: Prodigal
[2023-06-29 07:30:12,749] [INFO] Running command: gunzip -c /var/lib/cwl/stgdba0da16-062a-4dd0-af3c-df6344ece084/GCA_005878835.1_ASM587883v1_genomic.fna.gz | prodigal -d GCA_005878835.1_ASM587883v1_genomic.fna/cds.fna -a GCA_005878835.1_ASM587883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:30:24,215] [INFO] Task succeeded: Prodigal
[2023-06-29 07:30:24,215] [INFO] Task started: HMMsearch
[2023-06-29 07:30:24,216] [INFO] Running command: hmmsearch --tblout GCA_005878835.1_ASM587883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d957d6c-0451-4115-bb8a-a21c6a16d467/dqc_reference/reference_markers.hmm GCA_005878835.1_ASM587883v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:30:24,422] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:30:24,423] [INFO] Found 6/6 markers.
[2023-06-29 07:30:24,454] [INFO] Query marker FASTA was written to GCA_005878835.1_ASM587883v1_genomic.fna/markers.fasta
[2023-06-29 07:30:24,455] [INFO] Task started: Blastn
[2023-06-29 07:30:24,455] [INFO] Running command: blastn -query GCA_005878835.1_ASM587883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d957d6c-0451-4115-bb8a-a21c6a16d467/dqc_reference/reference_markers.fasta -out GCA_005878835.1_ASM587883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:30:25,377] [INFO] Task succeeded: Blastn
[2023-06-29 07:30:25,381] [INFO] Selected 30 target genomes.
[2023-06-29 07:30:25,381] [INFO] Target genome list was writen to GCA_005878835.1_ASM587883v1_genomic.fna/target_genomes.txt
[2023-06-29 07:30:25,382] [INFO] Task started: fastANI
[2023-06-29 07:30:25,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba0da16-062a-4dd0-af3c-df6344ece084/GCA_005878835.1_ASM587883v1_genomic.fna.gz --refList GCA_005878835.1_ASM587883v1_genomic.fna/target_genomes.txt --output GCA_005878835.1_ASM587883v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:30:44,700] [INFO] Task succeeded: fastANI
[2023-06-29 07:30:44,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d957d6c-0451-4115-bb8a-a21c6a16d467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:30:44,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d957d6c-0451-4115-bb8a-a21c6a16d467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:30:44,721] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:30:44,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 07:30:44,722] [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	77.0669	99	1304	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	77.0059	205	1304	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.93	207	1304	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.8293	195	1304	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.7581	199	1304	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.6354	177	1304	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.6156	145	1304	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.5675	220	1304	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.4507	213	1304	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.4274	224	1304	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	76.2864	87	1304	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.2853	133	1304	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.2678	176	1304	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.2597	183	1304	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	76.251	178	1304	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	76.2305	217	1304	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	76.2089	210	1304	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.1634	250	1304	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.0875	155	1304	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.0839	182	1304	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.0755	191	1304	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	76.0419	147	1304	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.0059	135	1304	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	75.9353	118	1304	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	75.9184	107	1304	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	75.7616	132	1304	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	75.728	128	1304	95	below_threshold
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	75.7107	93	1304	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	75.6048	105	1304	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	75.559	118	1304	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 07:30:44,724] [INFO] DFAST Taxonomy check result was written to GCA_005878835.1_ASM587883v1_genomic.fna/tc_result.tsv
[2023-06-29 07:30:44,724] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:30:44,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:30:44,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d957d6c-0451-4115-bb8a-a21c6a16d467/dqc_reference/checkm_data
[2023-06-29 07:30:44,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:30:44,764] [INFO] Task started: CheckM
[2023-06-29 07:30:44,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005878835.1_ASM587883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005878835.1_ASM587883v1_genomic.fna/checkm_input GCA_005878835.1_ASM587883v1_genomic.fna/checkm_result
[2023-06-29 07:31:21,832] [INFO] Task succeeded: CheckM
[2023-06-29 07:31:21,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 07:31:21,860] [INFO] ===== Completeness check finished =====
[2023-06-29 07:31:21,860] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:31:21,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005878835.1_ASM587883v1_genomic.fna/markers.fasta)
[2023-06-29 07:31:21,861] [INFO] Task started: Blastn
[2023-06-29 07:31:21,861] [INFO] Running command: blastn -query GCA_005878835.1_ASM587883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d957d6c-0451-4115-bb8a-a21c6a16d467/dqc_reference/reference_markers_gtdb.fasta -out GCA_005878835.1_ASM587883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:31:23,631] [INFO] Task succeeded: Blastn
[2023-06-29 07:31:23,634] [INFO] Selected 10 target genomes.
[2023-06-29 07:31:23,634] [INFO] Target genome list was writen to GCA_005878835.1_ASM587883v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:31:23,635] [INFO] Task started: fastANI
[2023-06-29 07:31:23,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba0da16-062a-4dd0-af3c-df6344ece084/GCA_005878835.1_ASM587883v1_genomic.fna.gz --refList GCA_005878835.1_ASM587883v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005878835.1_ASM587883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:31:31,034] [INFO] Task succeeded: fastANI
[2023-06-29 07:31:31,043] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 07:31:31,043] [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_005878835.1	s__13-2-20CM-66-19 sp005878835	100.0	1296	1304	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	conclusive
GCA_005878095.1	s__13-2-20CM-66-19 sp005878095	94.1223	914	1304	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	91.2544	675	1304	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_001914695.1	s__13-2-20CM-66-19 sp001914695	84.0927	702	1304	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_018240525.1	s__13-2-20CM-66-19 sp018240525	80.5466	585	1304	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_019235245.1	s__13-2-20CM-66-19 sp019235245	80.493	497	1304	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	80.3576	542	1304	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_005877705.1	s__13-2-20CM-66-19 sp005877705	80.1914	380	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	97.92	97.92	0.70	0.70	2	-
GCA_019242385.1	s__13-2-20CM-66-19 sp019242385	80.0398	362	1304	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_018241445.1	s__13-2-20CM-66-19 sp018241445	79.8729	500	1304	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	-
--------------------------------------------------------------------------------
[2023-06-29 07:31:31,045] [INFO] GTDB search result was written to GCA_005878835.1_ASM587883v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:31:31,046] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:31:31,071] [INFO] DFAST_QC result json was written to GCA_005878835.1_ASM587883v1_genomic.fna/dqc_result.json
[2023-06-29 07:31:31,071] [INFO] DFAST_QC completed!
[2023-06-29 07:31:31,071] [INFO] Total running time: 0h1m20s