[2023-07-01 01:12:51,312] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:12:51,318] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:12:51,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bc17823-f5dc-4d9f-9617-b94503b5f921/dqc_reference
[2023-07-01 01:12:52,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:12:52,681] [INFO] Task started: Prodigal
[2023-07-01 01:12:52,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg09c00f9d-eab5-4973-8a6d-16a543b3dc46/GCA_016871855.1_JGI_2017-08-21_genomic.fna.gz | prodigal -d GCA_016871855.1_JGI_2017-08-21_genomic.fna/cds.fna -a GCA_016871855.1_JGI_2017-08-21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:13:01,422] [INFO] Task succeeded: Prodigal
[2023-07-01 01:13:01,422] [INFO] Task started: HMMsearch
[2023-07-01 01:13:01,422] [INFO] Running command: hmmsearch --tblout GCA_016871855.1_JGI_2017-08-21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bc17823-f5dc-4d9f-9617-b94503b5f921/dqc_reference/reference_markers.hmm GCA_016871855.1_JGI_2017-08-21_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:13:01,672] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:13:01,673] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg09c00f9d-eab5-4973-8a6d-16a543b3dc46/GCA_016871855.1_JGI_2017-08-21_genomic.fna.gz]
[2023-07-01 01:13:01,706] [INFO] Query marker FASTA was written to GCA_016871855.1_JGI_2017-08-21_genomic.fna/markers.fasta
[2023-07-01 01:13:01,706] [INFO] Task started: Blastn
[2023-07-01 01:13:01,707] [INFO] Running command: blastn -query GCA_016871855.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bc17823-f5dc-4d9f-9617-b94503b5f921/dqc_reference/reference_markers.fasta -out GCA_016871855.1_JGI_2017-08-21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:13:02,363] [INFO] Task succeeded: Blastn
[2023-07-01 01:13:02,367] [INFO] Selected 11 target genomes.
[2023-07-01 01:13:02,368] [INFO] Target genome list was writen to GCA_016871855.1_JGI_2017-08-21_genomic.fna/target_genomes.txt
[2023-07-01 01:13:02,369] [INFO] Task started: fastANI
[2023-07-01 01:13:02,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c00f9d-eab5-4973-8a6d-16a543b3dc46/GCA_016871855.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016871855.1_JGI_2017-08-21_genomic.fna/target_genomes.txt --output GCA_016871855.1_JGI_2017-08-21_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:13:11,041] [INFO] Task succeeded: fastANI
[2023-07-01 01:13:11,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bc17823-f5dc-4d9f-9617-b94503b5f921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:13:11,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bc17823-f5dc-4d9f-9617-b94503b5f921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:13:11,052] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:13:11,052] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:13:11,052] [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	76.9038	345	907	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	76.8522	125	907	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	76.814	91	907	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	76.5057	132	907	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.8633	129	907	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.6992	131	907	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.6735	130	907	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	75.0898	61	907	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.9149	105	907	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:13:11,055] [INFO] DFAST Taxonomy check result was written to GCA_016871855.1_JGI_2017-08-21_genomic.fna/tc_result.tsv
[2023-07-01 01:13:11,055] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:13:11,056] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:13:11,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bc17823-f5dc-4d9f-9617-b94503b5f921/dqc_reference/checkm_data
[2023-07-01 01:13:11,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:13:11,091] [INFO] Task started: CheckM
[2023-07-01 01:13:11,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016871855.1_JGI_2017-08-21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016871855.1_JGI_2017-08-21_genomic.fna/checkm_input GCA_016871855.1_JGI_2017-08-21_genomic.fna/checkm_result
[2023-07-01 01:13:41,308] [INFO] Task succeeded: CheckM
[2023-07-01 01:13:41,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:13:41,334] [INFO] ===== Completeness check finished =====
[2023-07-01 01:13:41,334] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:13:41,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016871855.1_JGI_2017-08-21_genomic.fna/markers.fasta)
[2023-07-01 01:13:41,335] [INFO] Task started: Blastn
[2023-07-01 01:13:41,335] [INFO] Running command: blastn -query GCA_016871855.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bc17823-f5dc-4d9f-9617-b94503b5f921/dqc_reference/reference_markers_gtdb.fasta -out GCA_016871855.1_JGI_2017-08-21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:13:42,193] [INFO] Task succeeded: Blastn
[2023-07-01 01:13:42,198] [INFO] Selected 7 target genomes.
[2023-07-01 01:13:42,199] [INFO] Target genome list was writen to GCA_016871855.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:13:42,200] [INFO] Task started: fastANI
[2023-07-01 01:13:42,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c00f9d-eab5-4973-8a6d-16a543b3dc46/GCA_016871855.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016871855.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt --output GCA_016871855.1_JGI_2017-08-21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:13:47,084] [INFO] Task succeeded: fastANI
[2023-07-01 01:13:47,096] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:13:47,096] [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_016871855.1	s__PNKL01 sp016871855	100.0	904	907	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016218305.1	s__PNKL01 sp016218305	82.3462	406	907	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182795.1	s__PNKL01 sp016182795	81.859	581	907	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822425.1	s__PNKL01 sp013822425	81.6947	569	907	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825965.1	s__PNKF01 sp902825965	78.1624	284	907	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714015.1	s__PNKF01 sp016714015	78.1107	334	907	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874035.1	s__Fen-1231 sp016874035	77.3978	179	907	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:13:47,098] [INFO] GTDB search result was written to GCA_016871855.1_JGI_2017-08-21_genomic.fna/result_gtdb.tsv
[2023-07-01 01:13:47,099] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:13:47,104] [INFO] DFAST_QC result json was written to GCA_016871855.1_JGI_2017-08-21_genomic.fna/dqc_result.json
[2023-07-01 01:13:47,104] [INFO] DFAST_QC completed!
[2023-07-01 01:13:47,105] [INFO] Total running time: 0h0m56s