[2024-01-24 11:44:05,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,457] [INFO] DQC Reference Directory: /var/lib/cwl/stgfffe9ba5-a5f6-456f-ae1b-08291a55ca16/dqc_reference
[2024-01-24 11:44:08,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,840] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg33cfee0e-150e-446e-a185-bbad9be6c084/GCF_003148775.1_ASM314877v1_genomic.fna.gz | prodigal -d GCF_003148775.1_ASM314877v1_genomic.fna/cds.fna -a GCF_003148775.1_ASM314877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:21,631] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:21,631] [INFO] Task started: HMMsearch
[2024-01-24 11:44:21,631] [INFO] Running command: hmmsearch --tblout GCF_003148775.1_ASM314877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfffe9ba5-a5f6-456f-ae1b-08291a55ca16/dqc_reference/reference_markers.hmm GCF_003148775.1_ASM314877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:21,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:21,900] [INFO] Found 6/6 markers.
[2024-01-24 11:44:21,936] [INFO] Query marker FASTA was written to GCF_003148775.1_ASM314877v1_genomic.fna/markers.fasta
[2024-01-24 11:44:21,936] [INFO] Task started: Blastn
[2024-01-24 11:44:21,936] [INFO] Running command: blastn -query GCF_003148775.1_ASM314877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfffe9ba5-a5f6-456f-ae1b-08291a55ca16/dqc_reference/reference_markers.fasta -out GCF_003148775.1_ASM314877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:22,846] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:22,851] [INFO] Selected 22 target genomes.
[2024-01-24 11:44:22,851] [INFO] Target genome list was writen to GCF_003148775.1_ASM314877v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:22,860] [INFO] Task started: fastANI
[2024-01-24 11:44:22,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg33cfee0e-150e-446e-a185-bbad9be6c084/GCF_003148775.1_ASM314877v1_genomic.fna.gz --refList GCF_003148775.1_ASM314877v1_genomic.fna/target_genomes.txt --output GCF_003148775.1_ASM314877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:39,000] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:39,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfffe9ba5-a5f6-456f-ae1b-08291a55ca16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:39,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfffe9ba5-a5f6-456f-ae1b-08291a55ca16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:39,019] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:39,019] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:39,020] [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
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	79.8649	657	1328	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.9389	489	1328	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8532	484	1328	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	78.6773	494	1328	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.5358	444	1328	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	78.5172	481	1328	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	78.4653	464	1328	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.2693	405	1328	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.1739	396	1328	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.1629	382	1328	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.1481	399	1328	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	78.126	412	1328	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	78.1059	477	1328	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.956	418	1328	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.9531	418	1328	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9528	358	1328	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.9388	336	1328	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.8301	354	1328	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	77.8207	397	1328	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	77.7899	400	1328	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.7447	415	1328	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.5556	434	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:39,021] [INFO] DFAST Taxonomy check result was written to GCF_003148775.1_ASM314877v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:39,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:39,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:39,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfffe9ba5-a5f6-456f-ae1b-08291a55ca16/dqc_reference/checkm_data
[2024-01-24 11:44:39,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:39,064] [INFO] Task started: CheckM
[2024-01-24 11:44:39,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148775.1_ASM314877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148775.1_ASM314877v1_genomic.fna/checkm_input GCF_003148775.1_ASM314877v1_genomic.fna/checkm_result
[2024-01-24 11:45:23,644] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:23,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:23,663] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:23,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:23,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148775.1_ASM314877v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:23,665] [INFO] Task started: Blastn
[2024-01-24 11:45:23,665] [INFO] Running command: blastn -query GCF_003148775.1_ASM314877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfffe9ba5-a5f6-456f-ae1b-08291a55ca16/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148775.1_ASM314877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:25,407] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:25,420] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:25,420] [INFO] Target genome list was writen to GCF_003148775.1_ASM314877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:25,429] [INFO] Task started: fastANI
[2024-01-24 11:45:25,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg33cfee0e-150e-446e-a185-bbad9be6c084/GCF_003148775.1_ASM314877v1_genomic.fna.gz --refList GCF_003148775.1_ASM314877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148775.1_ASM314877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:34,281] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:34,300] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:34,300] [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_003148775.1	s__Roseicyclus mahoneyensis	100.0	1327	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018401055.1	s__Roseicyclus sp018401055	88.9844	896	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401965.1	s__Roseicyclus sp018401965	83.1603	644	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	82.6817	890	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	82.1785	761	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689735.1	s__Roseicyclus sp015689735	80.1633	622	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	80.0428	631	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	79.8818	655	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.8922	493	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	78.4908	515	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCA_015689705.1	s__HKCCE3408 sp015689705	78.4706	478	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:34,302] [INFO] GTDB search result was written to GCF_003148775.1_ASM314877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:34,303] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:34,306] [INFO] DFAST_QC result json was written to GCF_003148775.1_ASM314877v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:34,306] [INFO] DFAST_QC completed!
[2024-01-24 11:45:34,306] [INFO] Total running time: 0h1m29s