[2024-01-24 10:58:06,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ed8f2a2-8b0a-46a1-83a3-3fd0c0fda023/dqc_reference
[2024-01-24 10:58:09,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,633] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgc979550c-d0fb-4304-95ee-bd5d9c3e48b9/GCF_004362595.1_ASM436259v1_genomic.fna.gz | prodigal -d GCF_004362595.1_ASM436259v1_genomic.fna/cds.fna -a GCF_004362595.1_ASM436259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:23,726] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:23,726] [INFO] Task started: HMMsearch
[2024-01-24 10:58:23,726] [INFO] Running command: hmmsearch --tblout GCF_004362595.1_ASM436259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ed8f2a2-8b0a-46a1-83a3-3fd0c0fda023/dqc_reference/reference_markers.hmm GCF_004362595.1_ASM436259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:24,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:24,142] [INFO] Found 6/6 markers.
[2024-01-24 10:58:24,187] [INFO] Query marker FASTA was written to GCF_004362595.1_ASM436259v1_genomic.fna/markers.fasta
[2024-01-24 10:58:24,188] [INFO] Task started: Blastn
[2024-01-24 10:58:24,188] [INFO] Running command: blastn -query GCF_004362595.1_ASM436259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ed8f2a2-8b0a-46a1-83a3-3fd0c0fda023/dqc_reference/reference_markers.fasta -out GCF_004362595.1_ASM436259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:24,880] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:24,883] [INFO] Selected 21 target genomes.
[2024-01-24 10:58:24,883] [INFO] Target genome list was writen to GCF_004362595.1_ASM436259v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:24,931] [INFO] Task started: fastANI
[2024-01-24 10:58:24,932] [INFO] Running command: fastANI --query /var/lib/cwl/stgc979550c-d0fb-4304-95ee-bd5d9c3e48b9/GCF_004362595.1_ASM436259v1_genomic.fna.gz --refList GCF_004362595.1_ASM436259v1_genomic.fna/target_genomes.txt --output GCF_004362595.1_ASM436259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:43,520] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:43,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ed8f2a2-8b0a-46a1-83a3-3fd0c0fda023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:43,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ed8f2a2-8b0a-46a1-83a3-3fd0c0fda023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:43,537] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:43,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:43,538] [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
Bradymonas sediminis	strain=DSM 28820	GCA_004362595.1	1548548	1548548	type	True	100.0	1656	1656	95	conclusive
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	99.9945	1656	1656	95	conclusive
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	77.3447	481	1656	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	77.333	483	1656	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	76.612	200	1656	95	below_threshold
Lujinxingia sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	76.0327	158	1656	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	76.0172	150	1656	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	74.9377	50	1656	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.9104	74	1656	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	74.8768	53	1656	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	74.8621	69	1656	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	74.8066	52	1656	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.763	93	1656	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	74.6622	74	1656	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:43,539] [INFO] DFAST Taxonomy check result was written to GCF_004362595.1_ASM436259v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:43,540] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:43,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:43,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ed8f2a2-8b0a-46a1-83a3-3fd0c0fda023/dqc_reference/checkm_data
[2024-01-24 10:58:43,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:43,589] [INFO] Task started: CheckM
[2024-01-24 10:58:43,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362595.1_ASM436259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362595.1_ASM436259v1_genomic.fna/checkm_input GCF_004362595.1_ASM436259v1_genomic.fna/checkm_result
[2024-01-24 10:59:26,583] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:26,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:26,608] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:26,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:26,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362595.1_ASM436259v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:26,610] [INFO] Task started: Blastn
[2024-01-24 10:59:26,610] [INFO] Running command: blastn -query GCF_004362595.1_ASM436259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ed8f2a2-8b0a-46a1-83a3-3fd0c0fda023/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362595.1_ASM436259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:27,682] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:27,686] [INFO] Selected 25 target genomes.
[2024-01-24 10:59:27,686] [INFO] Target genome list was writen to GCF_004362595.1_ASM436259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:27,725] [INFO] Task started: fastANI
[2024-01-24 10:59:27,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgc979550c-d0fb-4304-95ee-bd5d9c3e48b9/GCF_004362595.1_ASM436259v1_genomic.fna.gz --refList GCF_004362595.1_ASM436259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362595.1_ASM436259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:48,412] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:48,432] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:48,432] [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_003258315.1	s__Bradymonas sediminis	99.9945	1656	1656	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Bradymonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_006517175.1	s__Persicimonas caeni	77.3284	483	1656	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007997015.1	s__Lujinxingia sp007997015	76.6346	198	1656	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007997005.1	s__Lujinxingia sp007997005	76.4886	212	1656	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260125.1	s__Lujinxingia litoralis	76.0279	149	1656	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005565.1	s__Lujinxingia sediminis	76.0233	159	1656	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	-
GCA_013697635.1	s__JACCWM01 sp013697635	75.7869	163	1656	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998715.1	s__JAGPDF01 sp017998715	74.9385	66	1656	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024805.1	s__Haliangium ochraceum	74.916	164	1656	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__Haliangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	74.9158	74	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016793095.1	s__JAEUJQ01 sp016793095	74.8202	110	1656	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	74.8117	65	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	74.8017	207	1656	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_017997455.1	s__JAGOEZ01 sp017997455	74.7965	52	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JAGOEZ01	95.0	98.60	98.27	0.77	0.77	3	-
GCA_018262455.1	s__JABFXX01 sp018262455	74.7117	68	1656	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005776735.1	s__SXON01 sp005776735	74.6369	65	1656	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:48,434] [INFO] GTDB search result was written to GCF_004362595.1_ASM436259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:48,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:48,439] [INFO] DFAST_QC result json was written to GCF_004362595.1_ASM436259v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:48,439] [INFO] DFAST_QC completed!
[2024-01-24 10:59:48,439] [INFO] Total running time: 0h1m42s