[2024-01-24 13:45:40,323] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:40,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:40,325] [INFO] DQC Reference Directory: /var/lib/cwl/stgac8407c2-15b2-48c6-85a0-e17598d607bb/dqc_reference
[2024-01-24 13:45:41,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:41,556] [INFO] Task started: Prodigal
[2024-01-24 13:45:41,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg417276e7-c5d4-4544-b9ac-1ab297f868f3/GCF_013340205.1_ASM1334020v1_genomic.fna.gz | prodigal -d GCF_013340205.1_ASM1334020v1_genomic.fna/cds.fna -a GCF_013340205.1_ASM1334020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:54,162] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:54,163] [INFO] Task started: HMMsearch
[2024-01-24 13:45:54,163] [INFO] Running command: hmmsearch --tblout GCF_013340205.1_ASM1334020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac8407c2-15b2-48c6-85a0-e17598d607bb/dqc_reference/reference_markers.hmm GCF_013340205.1_ASM1334020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:54,554] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:54,555] [INFO] Found 6/6 markers.
[2024-01-24 13:45:54,597] [INFO] Query marker FASTA was written to GCF_013340205.1_ASM1334020v1_genomic.fna/markers.fasta
[2024-01-24 13:45:54,598] [INFO] Task started: Blastn
[2024-01-24 13:45:54,598] [INFO] Running command: blastn -query GCF_013340205.1_ASM1334020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac8407c2-15b2-48c6-85a0-e17598d607bb/dqc_reference/reference_markers.fasta -out GCF_013340205.1_ASM1334020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:55,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:55,469] [INFO] Selected 27 target genomes.
[2024-01-24 13:45:55,470] [INFO] Target genome list was writen to GCF_013340205.1_ASM1334020v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:55,502] [INFO] Task started: fastANI
[2024-01-24 13:45:55,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg417276e7-c5d4-4544-b9ac-1ab297f868f3/GCF_013340205.1_ASM1334020v1_genomic.fna.gz --refList GCF_013340205.1_ASM1334020v1_genomic.fna/target_genomes.txt --output GCF_013340205.1_ASM1334020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:32,758] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:32,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac8407c2-15b2-48c6-85a0-e17598d607bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:32,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac8407c2-15b2-48c6-85a0-e17598d607bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:32,779] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:32,779] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:32,779] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	79.9889	929	1601	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	76.6262	324	1601	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	76.1784	397	1601	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	76.1217	440	1601	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	76.0812	426	1601	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	76.0494	411	1601	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	76.0129	452	1601	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	75.9959	431	1601	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	75.9802	458	1601	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	75.9628	494	1601	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.9184	484	1601	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	75.8547	497	1601	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.3233	311	1601	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.2979	323	1601	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.274	276	1601	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.2033	421	1601	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	75.1982	163	1601	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.1162	641	1601	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.0802	629	1601	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	75.0466	142	1601	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	74.9816	236	1601	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	74.9794	372	1601	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.945	236	1601	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	74.9177	309	1601	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	74.8967	312	1601	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	74.8615	393	1601	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	74.8498	409	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:32,781] [INFO] DFAST Taxonomy check result was written to GCF_013340205.1_ASM1334020v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:32,782] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:32,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:32,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac8407c2-15b2-48c6-85a0-e17598d607bb/dqc_reference/checkm_data
[2024-01-24 13:46:32,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:32,830] [INFO] Task started: CheckM
[2024-01-24 13:46:32,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013340205.1_ASM1334020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013340205.1_ASM1334020v1_genomic.fna/checkm_input GCF_013340205.1_ASM1334020v1_genomic.fna/checkm_result
[2024-01-24 13:47:17,108] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:17,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:17,129] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:17,129] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:17,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013340205.1_ASM1334020v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:17,130] [INFO] Task started: Blastn
[2024-01-24 13:47:17,131] [INFO] Running command: blastn -query GCF_013340205.1_ASM1334020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac8407c2-15b2-48c6-85a0-e17598d607bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013340205.1_ASM1334020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:18,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:18,614] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:18,615] [INFO] Target genome list was writen to GCF_013340205.1_ASM1334020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:18,644] [INFO] Task started: fastANI
[2024-01-24 13:47:18,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg417276e7-c5d4-4544-b9ac-1ab297f868f3/GCF_013340205.1_ASM1334020v1_genomic.fna.gz --refList GCF_013340205.1_ASM1334020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013340205.1_ASM1334020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:33,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:33,025] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:33,025] [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_013340205.1	s__R267 sp013340205	100.0	1598	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001768075.1	s__R267 sp001768075	80.5548	787	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	80.1337	921	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	80.0764	848	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022145.1	s__Anaeromyxobacter dehalogenans	80.0137	923	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	97.16	97.16	0.92	0.92	2	-
GCF_000017505.1	s__Anaeromyxobacter sp000017505	79.5695	856	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214955.1	s__JACRMN01 sp016214955	79.5649	845	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718565.1	s__JADKCZ01 sp016718565	79.1606	808	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JADKCZ01	95.0	99.81	99.81	0.97	0.97	2	-
GCA_903904005.1	s__CAIOAK01 sp903904005	79.1059	607	1601	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01	95.0	99.78	99.64	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:33,027] [INFO] GTDB search result was written to GCF_013340205.1_ASM1334020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:33,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:33,034] [INFO] DFAST_QC result json was written to GCF_013340205.1_ASM1334020v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:33,035] [INFO] DFAST_QC completed!
[2024-01-24 13:47:33,035] [INFO] Total running time: 0h1m53s