[2023-06-30 19:32:56,865] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:32:56,868] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:32:56,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c7d362d-006c-4528-a092-4fd6eeb5397c/dqc_reference
[2023-06-30 19:32:58,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:32:58,501] [INFO] Task started: Prodigal
[2023-06-30 19:32:58,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg31790951-2451-481c-838b-b84a552c2020/GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna.gz | prodigal -d GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/cds.fna -a GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:33:05,735] [INFO] Task succeeded: Prodigal
[2023-06-30 19:33:05,736] [INFO] Task started: HMMsearch
[2023-06-30 19:33:05,736] [INFO] Running command: hmmsearch --tblout GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c7d362d-006c-4528-a092-4fd6eeb5397c/dqc_reference/reference_markers.hmm GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:33:06,007] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:33:06,008] [INFO] Found 6/6 markers.
[2023-06-30 19:33:06,038] [INFO] Query marker FASTA was written to GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/markers.fasta
[2023-06-30 19:33:06,038] [INFO] Task started: Blastn
[2023-06-30 19:33:06,039] [INFO] Running command: blastn -query GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c7d362d-006c-4528-a092-4fd6eeb5397c/dqc_reference/reference_markers.fasta -out GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:33:07,105] [INFO] Task succeeded: Blastn
[2023-06-30 19:33:07,110] [INFO] Selected 35 target genomes.
[2023-06-30 19:33:07,110] [INFO] Target genome list was writen to GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/target_genomes.txt
[2023-06-30 19:33:07,117] [INFO] Task started: fastANI
[2023-06-30 19:33:07,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg31790951-2451-481c-838b-b84a552c2020/GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna.gz --refList GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/target_genomes.txt --output GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:33:39,125] [INFO] Task succeeded: fastANI
[2023-06-30 19:33:39,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c7d362d-006c-4528-a092-4fd6eeb5397c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:33:39,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c7d362d-006c-4528-a092-4fd6eeb5397c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:33:39,151] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:33:39,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:33:39,151] [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
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	77.2648	121	655	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	77.0836	119	655	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	77.0783	122	655	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	77.0222	117	655	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.9809	128	655	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.8085	126	655	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	76.7217	110	655	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	76.6871	124	655	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	76.6529	110	655	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	76.6329	135	655	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	76.6263	142	655	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	76.6172	125	655	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	76.6156	117	655	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	76.5885	126	655	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	76.5877	115	655	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	76.5745	118	655	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	76.5389	122	655	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	76.5359	113	655	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	76.5279	129	655	95	below_threshold
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	76.5254	109	655	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	76.5229	95	655	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	76.4613	112	655	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	76.4407	121	655	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	76.4216	127	655	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	76.4069	86	655	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	76.3959	97	655	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	76.3819	127	655	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.3596	118	655	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	76.2952	96	655	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	76.2011	94	655	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	76.1225	112	655	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	76.1016	103	655	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	76.0774	107	655	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	75.9824	120	655	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	75.9532	120	655	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:33:39,153] [INFO] DFAST Taxonomy check result was written to GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/tc_result.tsv
[2023-06-30 19:33:39,154] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:33:39,154] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:33:39,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c7d362d-006c-4528-a092-4fd6eeb5397c/dqc_reference/checkm_data
[2023-06-30 19:33:39,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:33:39,188] [INFO] Task started: CheckM
[2023-06-30 19:33:39,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/checkm_input GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/checkm_result
[2023-06-30 19:34:05,668] [INFO] Task succeeded: CheckM
[2023-06-30 19:34:05,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:34:05,693] [INFO] ===== Completeness check finished =====
[2023-06-30 19:34:05,694] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:34:05,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/markers.fasta)
[2023-06-30 19:34:05,695] [INFO] Task started: Blastn
[2023-06-30 19:34:05,695] [INFO] Running command: blastn -query GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c7d362d-006c-4528-a092-4fd6eeb5397c/dqc_reference/reference_markers_gtdb.fasta -out GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:34:07,386] [INFO] Task succeeded: Blastn
[2023-06-30 19:34:07,391] [INFO] Selected 13 target genomes.
[2023-06-30 19:34:07,392] [INFO] Target genome list was writen to GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:34:07,416] [INFO] Task started: fastANI
[2023-06-30 19:34:07,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg31790951-2451-481c-838b-b84a552c2020/GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna.gz --refList GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/target_genomes_gtdb.txt --output GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:34:15,637] [INFO] Task succeeded: fastANI
[2023-06-30 19:34:15,652] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:34:15,652] [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_903954205.1	s__Mxb001 sp903954205	98.2605	445	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	98.46	98.20	0.79	0.70	14	conclusive
GCA_016870425.1	s__Mxb001 sp016870425	81.7147	416	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379115.1	s__Mxb001 sp004379115	80.02	315	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870515.1	s__Mxb001 sp016870515	79.4185	334	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848435.1	s__Mxb001 sp903848435	79.2841	236	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	96.93	95.89	0.80	0.74	3	-
GCA_903909555.1	s__Mxb001 sp903909555	79.09	310	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	99.15	99.05	0.83	0.81	4	-
GCA_903934925.1	s__UBA10649 sp903934925	77.9061	148	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	99.42	99.35	0.85	0.83	4	-
GCA_016717115.1	s__UBA10649 sp016717115	77.8632	165	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856385.1	s__UBA10649 sp017856385	77.5531	170	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	76.9013	100	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916455.1	s__Nocardioides sp017916455	76.738	103	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_900659615.1	s__Spirillospora fibrosa	76.0594	116	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208105.1	s__Spirillospora coerulea	75.981	120	655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-30 19:34:15,690] [INFO] GTDB search result was written to GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/result_gtdb.tsv
[2023-06-30 19:34:15,691] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:34:15,697] [INFO] DFAST_QC result json was written to GCA_903953595.1_freshwater_MAG_---_Loc090519-4m_bin-561_genomic.fna/dqc_result.json
[2023-06-30 19:34:15,698] [INFO] DFAST_QC completed!
[2023-06-30 19:34:15,698] [INFO] Total running time: 0h1m19s