[2023-06-29 14:43:28,441] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:43:28,448] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:43:28,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg3daa954b-83bd-4094-a5f7-e6e26fa468b9/dqc_reference
[2023-06-29 14:43:29,778] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:43:29,779] [INFO] Task started: Prodigal
[2023-06-29 14:43:29,779] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0e94e57-dda1-4c57-abcc-1c02bdae235e/GCA_021774435.1_ASM2177443v1_genomic.fna.gz | prodigal -d GCA_021774435.1_ASM2177443v1_genomic.fna/cds.fna -a GCA_021774435.1_ASM2177443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:43:49,310] [INFO] Task succeeded: Prodigal
[2023-06-29 14:43:49,310] [INFO] Task started: HMMsearch
[2023-06-29 14:43:49,310] [INFO] Running command: hmmsearch --tblout GCA_021774435.1_ASM2177443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3daa954b-83bd-4094-a5f7-e6e26fa468b9/dqc_reference/reference_markers.hmm GCA_021774435.1_ASM2177443v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:43:49,660] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:43:49,662] [INFO] Found 6/6 markers.
[2023-06-29 14:43:49,726] [INFO] Query marker FASTA was written to GCA_021774435.1_ASM2177443v1_genomic.fna/markers.fasta
[2023-06-29 14:43:49,726] [INFO] Task started: Blastn
[2023-06-29 14:43:49,726] [INFO] Running command: blastn -query GCA_021774435.1_ASM2177443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3daa954b-83bd-4094-a5f7-e6e26fa468b9/dqc_reference/reference_markers.fasta -out GCA_021774435.1_ASM2177443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:43:50,434] [INFO] Task succeeded: Blastn
[2023-06-29 14:43:50,439] [INFO] Selected 37 target genomes.
[2023-06-29 14:43:50,440] [INFO] Target genome list was writen to GCA_021774435.1_ASM2177443v1_genomic.fna/target_genomes.txt
[2023-06-29 14:43:50,445] [INFO] Task started: fastANI
[2023-06-29 14:43:50,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e94e57-dda1-4c57-abcc-1c02bdae235e/GCA_021774435.1_ASM2177443v1_genomic.fna.gz --refList GCA_021774435.1_ASM2177443v1_genomic.fna/target_genomes.txt --output GCA_021774435.1_ASM2177443v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:44:17,030] [INFO] Task succeeded: fastANI
[2023-06-29 14:44:17,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3daa954b-83bd-4094-a5f7-e6e26fa468b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:44:17,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3daa954b-83bd-4094-a5f7-e6e26fa468b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:44:17,045] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:44:17,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:44:17,046] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.839	64	2163	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.5711	51	2163	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.252	68	2163	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.2505	60	2163	95	below_threshold
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	75.222	53	2163	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.1931	55	2163	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.1279	60	2163	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	75.0982	58	2163	95	below_threshold
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	75.0382	52	2163	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:44:17,048] [INFO] DFAST Taxonomy check result was written to GCA_021774435.1_ASM2177443v1_genomic.fna/tc_result.tsv
[2023-06-29 14:44:17,048] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:44:17,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:44:17,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3daa954b-83bd-4094-a5f7-e6e26fa468b9/dqc_reference/checkm_data
[2023-06-29 14:44:17,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:44:17,122] [INFO] Task started: CheckM
[2023-06-29 14:44:17,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021774435.1_ASM2177443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021774435.1_ASM2177443v1_genomic.fna/checkm_input GCA_021774435.1_ASM2177443v1_genomic.fna/checkm_result
[2023-06-29 14:45:14,559] [INFO] Task succeeded: CheckM
[2023-06-29 14:45:14,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:45:14,586] [INFO] ===== Completeness check finished =====
[2023-06-29 14:45:14,586] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:45:14,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021774435.1_ASM2177443v1_genomic.fna/markers.fasta)
[2023-06-29 14:45:14,587] [INFO] Task started: Blastn
[2023-06-29 14:45:14,587] [INFO] Running command: blastn -query GCA_021774435.1_ASM2177443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3daa954b-83bd-4094-a5f7-e6e26fa468b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_021774435.1_ASM2177443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:45:15,578] [INFO] Task succeeded: Blastn
[2023-06-29 14:45:15,599] [INFO] Selected 35 target genomes.
[2023-06-29 14:45:15,599] [INFO] Target genome list was writen to GCA_021774435.1_ASM2177443v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:45:15,618] [INFO] Task started: fastANI
[2023-06-29 14:45:15,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e94e57-dda1-4c57-abcc-1c02bdae235e/GCA_021774435.1_ASM2177443v1_genomic.fna.gz --refList GCA_021774435.1_ASM2177443v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021774435.1_ASM2177443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:45:40,076] [INFO] Task succeeded: fastANI
[2023-06-29 14:45:40,092] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:45:40,093] [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_012103325.1	s__GCA-2717185 sp012103325	78.788	768	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937525.1	s__MarineAlpha4-Bin1 sp002937525	76.1947	107	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__MarineAlpha4-Bin1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_018665505.1	s__UBA6544 sp018665505	75.9344	81	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	75.6082	87	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197755.1	s__Ferrovibrio terrae	75.5711	51	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	75.5423	53	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	75.4012	51	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.3669	71	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005845.1	s__Hwanghaeella grinnelliae	75.222	53	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163145.1	s__Roseomonas_A frigidaquae	75.1199	56	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005222815.1	s__Roseomonas_A sp005222815	75.1047	61	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716125.1	s__UBA6544 sp002716125	75.0953	71	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220095.1	s__Bosea sp002220095	75.0512	54	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151425.1	s__Palsa-883 sp003151425	74.7133	57	2163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Palsa-883	95.0	99.82	99.82	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:45:40,095] [INFO] GTDB search result was written to GCA_021774435.1_ASM2177443v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:45:40,095] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:45:40,099] [INFO] DFAST_QC result json was written to GCA_021774435.1_ASM2177443v1_genomic.fna/dqc_result.json
[2023-06-29 14:45:40,100] [INFO] DFAST_QC completed!
[2023-06-29 14:45:40,100] [INFO] Total running time: 0h2m12s