[2024-01-25 20:18:06,067] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:06,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:06,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg3db3d81c-1e7c-4014-8def-191ea99deaf6/dqc_reference
[2024-01-25 20:18:07,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:07,246] [INFO] Task started: Prodigal
[2024-01-25 20:18:07,246] [INFO] Running command: gunzip -c /var/lib/cwl/stga94bf4f2-8afb-4994-8743-40eb8249f07b/GCF_026013545.1_ASM2601354v1_genomic.fna.gz | prodigal -d GCF_026013545.1_ASM2601354v1_genomic.fna/cds.fna -a GCF_026013545.1_ASM2601354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:19,292] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:19,293] [INFO] Task started: HMMsearch
[2024-01-25 20:18:19,293] [INFO] Running command: hmmsearch --tblout GCF_026013545.1_ASM2601354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3db3d81c-1e7c-4014-8def-191ea99deaf6/dqc_reference/reference_markers.hmm GCF_026013545.1_ASM2601354v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:19,563] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:19,564] [INFO] Found 6/6 markers.
[2024-01-25 20:18:19,606] [INFO] Query marker FASTA was written to GCF_026013545.1_ASM2601354v1_genomic.fna/markers.fasta
[2024-01-25 20:18:19,606] [INFO] Task started: Blastn
[2024-01-25 20:18:19,606] [INFO] Running command: blastn -query GCF_026013545.1_ASM2601354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db3d81c-1e7c-4014-8def-191ea99deaf6/dqc_reference/reference_markers.fasta -out GCF_026013545.1_ASM2601354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:20,566] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:20,571] [INFO] Selected 25 target genomes.
[2024-01-25 20:18:20,571] [INFO] Target genome list was writen to GCF_026013545.1_ASM2601354v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:20,599] [INFO] Task started: fastANI
[2024-01-25 20:18:20,599] [INFO] Running command: fastANI --query /var/lib/cwl/stga94bf4f2-8afb-4994-8743-40eb8249f07b/GCF_026013545.1_ASM2601354v1_genomic.fna.gz --refList GCF_026013545.1_ASM2601354v1_genomic.fna/target_genomes.txt --output GCF_026013545.1_ASM2601354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:39,983] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:39,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3db3d81c-1e7c-4014-8def-191ea99deaf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:39,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3db3d81c-1e7c-4014-8def-191ea99deaf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:39,998] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:18:39,998] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:18:39,998] [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
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	81.1335	794	1627	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.9118	552	1627	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.8279	584	1627	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	79.8087	579	1627	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.7383	547	1627	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	79.6682	586	1627	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.6374	529	1627	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	79.6338	587	1627	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.5301	532	1627	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	79.158	584	1627	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	79.1357	555	1627	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	79.1171	581	1627	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	79.1019	587	1627	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.0874	562	1627	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.0575	563	1627	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	78.8403	515	1627	95	below_threshold
Albidovulum inexpectatum	strain=DSM 12048	GCA_002927635.1	196587	196587	type	True	78.8373	471	1627	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.8136	493	1627	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	78.6069	454	1627	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5393	483	1627	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.456	484	1627	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	78.3757	413	1627	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.0613	361	1627	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8185	355	1627	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7162	339	1627	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:40,000] [INFO] DFAST Taxonomy check result was written to GCF_026013545.1_ASM2601354v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:40,000] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:40,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:40,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3db3d81c-1e7c-4014-8def-191ea99deaf6/dqc_reference/checkm_data
[2024-01-25 20:18:40,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:40,049] [INFO] Task started: CheckM
[2024-01-25 20:18:40,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026013545.1_ASM2601354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026013545.1_ASM2601354v1_genomic.fna/checkm_input GCF_026013545.1_ASM2601354v1_genomic.fna/checkm_result
[2024-01-25 20:19:18,871] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:18,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:18,893] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:18,893] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:18,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026013545.1_ASM2601354v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:18,893] [INFO] Task started: Blastn
[2024-01-25 20:19:18,893] [INFO] Running command: blastn -query GCF_026013545.1_ASM2601354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db3d81c-1e7c-4014-8def-191ea99deaf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_026013545.1_ASM2601354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:20,653] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:20,656] [INFO] Selected 14 target genomes.
[2024-01-25 20:19:20,656] [INFO] Target genome list was writen to GCF_026013545.1_ASM2601354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:20,676] [INFO] Task started: fastANI
[2024-01-25 20:19:20,676] [INFO] Running command: fastANI --query /var/lib/cwl/stga94bf4f2-8afb-4994-8743-40eb8249f07b/GCF_026013545.1_ASM2601354v1_genomic.fna.gz --refList GCF_026013545.1_ASM2601354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026013545.1_ASM2601354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:32,168] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:32,177] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:19:32,178] [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_011620265.1	s__Albidovulum sp011620265	83.3692	774	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	82.628	803	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933605.1	s__Albidovulum sp008933605	81.667	679	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302475.1	s__Albidovulum aquaemixtae	81.1031	798	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841115.1	s__Albidovulum sp002841115	81.064	632	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973535.1	s__Albidovulum denitrificans	80.444	717	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	80.2527	607	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCA_002440625.1	s__Albidovulum sp002440625	79.9111	582	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	79.7959	580	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022265.1	s__Paenirhodobacter ferrireducens	79.608	589	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.5177	560	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.0674	562	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002927635.1	s__Albidovulum inexpectatum	78.8283	472	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	78.6062	453	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:32,179] [INFO] GTDB search result was written to GCF_026013545.1_ASM2601354v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:32,180] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:32,183] [INFO] DFAST_QC result json was written to GCF_026013545.1_ASM2601354v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:32,183] [INFO] DFAST_QC completed!
[2024-01-25 20:19:32,183] [INFO] Total running time: 0h1m26s