[2024-01-24 12:29:27,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:27,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:27,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg1af3f573-71af-444a-9edf-c2fb8dfd09dc/dqc_reference
[2024-01-24 12:29:28,810] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:28,811] [INFO] Task started: Prodigal
[2024-01-24 12:29:28,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e7800dd-80bb-43fd-8eae-5f481abb4e28/GCF_000522985.1_ASM52298v1_genomic.fna.gz | prodigal -d GCF_000522985.1_ASM52298v1_genomic.fna/cds.fna -a GCF_000522985.1_ASM52298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:50,538] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:50,539] [INFO] Task started: HMMsearch
[2024-01-24 12:29:50,539] [INFO] Running command: hmmsearch --tblout GCF_000522985.1_ASM52298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1af3f573-71af-444a-9edf-c2fb8dfd09dc/dqc_reference/reference_markers.hmm GCF_000522985.1_ASM52298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:51,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:51,036] [INFO] Found 6/6 markers.
[2024-01-24 12:29:51,109] [INFO] Query marker FASTA was written to GCF_000522985.1_ASM52298v1_genomic.fna/markers.fasta
[2024-01-24 12:29:51,110] [INFO] Task started: Blastn
[2024-01-24 12:29:51,110] [INFO] Running command: blastn -query GCF_000522985.1_ASM52298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af3f573-71af-444a-9edf-c2fb8dfd09dc/dqc_reference/reference_markers.fasta -out GCF_000522985.1_ASM52298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:51,991] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:51,994] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:51,995] [INFO] Target genome list was writen to GCF_000522985.1_ASM52298v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:52,002] [INFO] Task started: fastANI
[2024-01-24 12:29:52,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7800dd-80bb-43fd-8eae-5f481abb4e28/GCF_000522985.1_ASM52298v1_genomic.fna.gz --refList GCF_000522985.1_ASM52298v1_genomic.fna/target_genomes.txt --output GCF_000522985.1_ASM52298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:14,638] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:14,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1af3f573-71af-444a-9edf-c2fb8dfd09dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:14,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1af3f573-71af-444a-9edf-c2fb8dfd09dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:14,651] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:14,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:14,651] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	100.0	2478	2490	95	conclusive
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	76.8719	224	2490	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	76.3161	194	2490	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	76.3126	341	2490	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.5954	405	2490	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.1485	72	2490	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.0394	60	2490	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.9106	724	2490	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.8715	703	2490	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	74.8619	154	2490	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	74.8346	227	2490	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	74.82	497	2490	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	74.8125	510	2490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:14,653] [INFO] DFAST Taxonomy check result was written to GCF_000522985.1_ASM52298v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:14,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:14,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:14,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1af3f573-71af-444a-9edf-c2fb8dfd09dc/dqc_reference/checkm_data
[2024-01-24 12:30:14,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:14,731] [INFO] Task started: CheckM
[2024-01-24 12:30:14,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000522985.1_ASM52298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000522985.1_ASM52298v1_genomic.fna/checkm_input GCF_000522985.1_ASM52298v1_genomic.fna/checkm_result
[2024-01-24 12:31:24,791] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:24,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:24,819] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:24,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:24,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000522985.1_ASM52298v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:24,820] [INFO] Task started: Blastn
[2024-01-24 12:31:24,821] [INFO] Running command: blastn -query GCF_000522985.1_ASM52298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af3f573-71af-444a-9edf-c2fb8dfd09dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000522985.1_ASM52298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:26,397] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:26,401] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:26,401] [INFO] Target genome list was writen to GCF_000522985.1_ASM52298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:26,440] [INFO] Task started: fastANI
[2024-01-24 12:31:26,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7800dd-80bb-43fd-8eae-5f481abb4e28/GCF_000522985.1_ASM52298v1_genomic.fna.gz --refList GCF_000522985.1_ASM52298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000522985.1_ASM52298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:45,285] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:45,298] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:45,299] [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_000522985.1	s__Gemmatirosa kalamazoonesis	100.0	2482	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatirosa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013361745.1	s__JABFXC01 sp013361745	77.7573	396	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016194585.1	s__Fen-1231 sp016194585	77.5949	564	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.33	99.33	0.81	0.81	2	-
GCA_013361935.1	s__JABFXC01 sp013361935	77.5696	670	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	99.88	99.88	0.94	0.92	3	-
GCA_003223455.1	s__AG11 sp003223455	77.5566	705	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361335.1	s__AG11 sp013361335	77.4757	588	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	99.60	99.48	0.90	0.83	7	-
GCA_016871915.1	s__PNKF01 sp016871915	77.384	196	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	99.71	99.71	0.88	0.88	2	-
GCA_016191225.1	s__JACPPC01 sp016191225	77.1701	452	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACPPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003171215.1	s__Fen-1231 sp003171215	76.961	435	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	97.59	95.49	0.88	0.84	3	-
GCA_016714015.1	s__PNKF01 sp016714015	76.9071	579	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817305.1	s__JACDCY01 sp013817305	76.8558	193	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACDCY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825965.1	s__PNKF01 sp902825965	76.8064	451	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200495.1	s__JACPPC01 sp016200495	76.7941	586	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACPPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719105.1	s__SCN-70-22 sp016719105	76.4592	581	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	98.70	98.52	0.93	0.89	8	-
GCA_014379355.1	s__JACMLX01 sp014379355	76.0022	296	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACMLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805735.1	s__Longimicrobium sp902805735	75.5687	394	2490	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__Longimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:45,300] [INFO] GTDB search result was written to GCF_000522985.1_ASM52298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:45,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:45,304] [INFO] DFAST_QC result json was written to GCF_000522985.1_ASM52298v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:45,304] [INFO] DFAST_QC completed!
[2024-01-24 12:31:45,305] [INFO] Total running time: 0h2m18s