[2023-06-27 18:42:31,967] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:42:31,969] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:42:31,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f961f6d-8202-41f1-845d-f25c634e8f7f/dqc_reference
[2023-06-27 18:42:35,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:42:35,269] [INFO] Task started: Prodigal
[2023-06-27 18:42:35,270] [INFO] Running command: gunzip -c /var/lib/cwl/stg1956be14-f704-44e5-aa8e-b88c1a8faa77/GCA_026708215.1_ASM2670821v1_genomic.fna.gz | prodigal -d GCA_026708215.1_ASM2670821v1_genomic.fna/cds.fna -a GCA_026708215.1_ASM2670821v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:42:45,300] [INFO] Task succeeded: Prodigal
[2023-06-27 18:42:45,301] [INFO] Task started: HMMsearch
[2023-06-27 18:42:45,301] [INFO] Running command: hmmsearch --tblout GCA_026708215.1_ASM2670821v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f961f6d-8202-41f1-845d-f25c634e8f7f/dqc_reference/reference_markers.hmm GCA_026708215.1_ASM2670821v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:42:45,551] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:42:45,552] [INFO] Found 6/6 markers.
[2023-06-27 18:42:45,588] [INFO] Query marker FASTA was written to GCA_026708215.1_ASM2670821v1_genomic.fna/markers.fasta
[2023-06-27 18:42:45,589] [INFO] Task started: Blastn
[2023-06-27 18:42:45,589] [INFO] Running command: blastn -query GCA_026708215.1_ASM2670821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f961f6d-8202-41f1-845d-f25c634e8f7f/dqc_reference/reference_markers.fasta -out GCA_026708215.1_ASM2670821v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:42:46,348] [INFO] Task succeeded: Blastn
[2023-06-27 18:42:46,352] [INFO] Selected 28 target genomes.
[2023-06-27 18:42:46,352] [INFO] Target genome list was writen to GCA_026708215.1_ASM2670821v1_genomic.fna/target_genomes.txt
[2023-06-27 18:42:46,353] [INFO] Task started: fastANI
[2023-06-27 18:42:46,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg1956be14-f704-44e5-aa8e-b88c1a8faa77/GCA_026708215.1_ASM2670821v1_genomic.fna.gz --refList GCA_026708215.1_ASM2670821v1_genomic.fna/target_genomes.txt --output GCA_026708215.1_ASM2670821v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:43:06,424] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:06,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f961f6d-8202-41f1-845d-f25c634e8f7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:43:06,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f961f6d-8202-41f1-845d-f25c634e8f7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:43:06,443] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:43:06,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:43:06,444] [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
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	75.8159	57	1106	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.76	70	1106	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.7384	63	1106	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	75.6798	62	1106	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.6784	65	1106	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	75.5381	56	1106	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	75.4931	80	1106	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.4287	124	1106	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.4174	125	1106	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.3909	81	1106	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	75.3476	56	1106	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	75.3275	56	1106	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	75.2788	56	1106	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.0026	66	1106	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:43:06,446] [INFO] DFAST Taxonomy check result was written to GCA_026708215.1_ASM2670821v1_genomic.fna/tc_result.tsv
[2023-06-27 18:43:06,446] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:43:06,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:43:06,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f961f6d-8202-41f1-845d-f25c634e8f7f/dqc_reference/checkm_data
[2023-06-27 18:43:06,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:43:06,483] [INFO] Task started: CheckM
[2023-06-27 18:43:06,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708215.1_ASM2670821v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708215.1_ASM2670821v1_genomic.fna/checkm_input GCA_026708215.1_ASM2670821v1_genomic.fna/checkm_result
[2023-06-27 18:43:39,302] [INFO] Task succeeded: CheckM
[2023-06-27 18:43:39,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:43:39,330] [INFO] ===== Completeness check finished =====
[2023-06-27 18:43:39,330] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:43:39,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708215.1_ASM2670821v1_genomic.fna/markers.fasta)
[2023-06-27 18:43:39,331] [INFO] Task started: Blastn
[2023-06-27 18:43:39,331] [INFO] Running command: blastn -query GCA_026708215.1_ASM2670821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f961f6d-8202-41f1-845d-f25c634e8f7f/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708215.1_ASM2670821v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:43:40,501] [INFO] Task succeeded: Blastn
[2023-06-27 18:43:40,506] [INFO] Selected 25 target genomes.
[2023-06-27 18:43:40,506] [INFO] Target genome list was writen to GCA_026708215.1_ASM2670821v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:43:40,532] [INFO] Task started: fastANI
[2023-06-27 18:43:40,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg1956be14-f704-44e5-aa8e-b88c1a8faa77/GCA_026708215.1_ASM2670821v1_genomic.fna.gz --refList GCA_026708215.1_ASM2670821v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708215.1_ASM2670821v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:43:57,916] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:57,936] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 18:43:57,936] [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_009839325.1	s__VXPW01 sp009839325	98.5423	798	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VXPW01;f__VXPW01;g__VXPW01	95.0	99.26	99.26	0.90	0.90	2	conclusive
GCA_900197615.1	s__Bin65 sp900197615	77.1926	77	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721365.1	s__GCA-2721365 sp002721365	76.0363	65	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	75.7088	64	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_018432935.1	s__JAHDSF01 sp018432935	75.7077	60	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	75.6371	67	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	75.6199	73	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217615.1	s__Methylobacterium sp003217615	75.5307	54	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016792605.1	s__JAEULC01 sp016792605	75.5207	59	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULC01;f__JAEULC01;g__JAEULC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	75.4971	58	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380075.1	s__WHSO01 sp009380075	75.4944	51	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__WHSO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.4323	123	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_009720755.1	s__Rhodoplanes serenus	75.3535	80	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCF_008040045.1	s__Methylobacterium sp008040045	75.2817	58	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_016595245.1	s__Azospirillum sp016595245	75.2422	77	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982615.1	s__Roseomonas deserti	74.9978	66	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:43:57,939] [INFO] GTDB search result was written to GCA_026708215.1_ASM2670821v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:43:57,939] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:43:57,944] [INFO] DFAST_QC result json was written to GCA_026708215.1_ASM2670821v1_genomic.fna/dqc_result.json
[2023-06-27 18:43:57,944] [INFO] DFAST_QC completed!
[2023-06-27 18:43:57,944] [INFO] Total running time: 0h1m26s