[2024-01-24 14:28:18,492] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaba67a0-f31a-4536-a603-4a585b12ca50/dqc_reference
[2024-01-24 14:28:20,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,485] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,486] [INFO] Running command: gunzip -c /var/lib/cwl/stgbae759c7-fcf5-4459-b798-12eaae42e0d5/GCF_007997015.1_ASM799701v1_genomic.fna.gz | prodigal -d GCF_007997015.1_ASM799701v1_genomic.fna/cds.fna -a GCF_007997015.1_ASM799701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:37,653] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:37,654] [INFO] Task started: HMMsearch
[2024-01-24 14:28:37,654] [INFO] Running command: hmmsearch --tblout GCF_007997015.1_ASM799701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaba67a0-f31a-4536-a603-4a585b12ca50/dqc_reference/reference_markers.hmm GCF_007997015.1_ASM799701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:38,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:38,039] [INFO] Found 6/6 markers.
[2024-01-24 14:28:38,086] [INFO] Query marker FASTA was written to GCF_007997015.1_ASM799701v1_genomic.fna/markers.fasta
[2024-01-24 14:28:38,086] [INFO] Task started: Blastn
[2024-01-24 14:28:38,087] [INFO] Running command: blastn -query GCF_007997015.1_ASM799701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaba67a0-f31a-4536-a603-4a585b12ca50/dqc_reference/reference_markers.fasta -out GCF_007997015.1_ASM799701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:38,808] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:38,846] [INFO] Selected 19 target genomes.
[2024-01-24 14:28:38,847] [INFO] Target genome list was writen to GCF_007997015.1_ASM799701v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:38,860] [INFO] Task started: fastANI
[2024-01-24 14:28:38,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae759c7-fcf5-4459-b798-12eaae42e0d5/GCF_007997015.1_ASM799701v1_genomic.fna.gz --refList GCF_007997015.1_ASM799701v1_genomic.fna/target_genomes.txt --output GCF_007997015.1_ASM799701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:55,525] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:55,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaba67a0-f31a-4536-a603-4a585b12ca50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:55,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaba67a0-f31a-4536-a603-4a585b12ca50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:55,536] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:55,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:55,537] [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
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	100.0	1816	1817	95	conclusive
Lujinxingia sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	87.3989	1534	1817	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	81.5732	1209	1817	95	below_threshold
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	76.6927	203	1817	95	below_threshold
Bradymonas sediminis	strain=DSM 28820	GCA_004362595.1	1548548	1548548	type	True	76.6925	202	1817	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	76.6333	337	1817	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	76.6139	339	1817	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	75.106	53	1817	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	74.9589	149	1817	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	74.8965	77	1817	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	74.8916	78	1817	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.724	103	1817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:55,539] [INFO] DFAST Taxonomy check result was written to GCF_007997015.1_ASM799701v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:55,539] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:55,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:55,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaba67a0-f31a-4536-a603-4a585b12ca50/dqc_reference/checkm_data
[2024-01-24 14:28:55,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:55,603] [INFO] Task started: CheckM
[2024-01-24 14:28:55,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007997015.1_ASM799701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007997015.1_ASM799701v1_genomic.fna/checkm_input GCF_007997015.1_ASM799701v1_genomic.fna/checkm_result
[2024-01-24 14:29:44,944] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:44,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:44,969] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:44,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:44,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007997015.1_ASM799701v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:44,970] [INFO] Task started: Blastn
[2024-01-24 14:29:44,971] [INFO] Running command: blastn -query GCF_007997015.1_ASM799701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaba67a0-f31a-4536-a603-4a585b12ca50/dqc_reference/reference_markers_gtdb.fasta -out GCF_007997015.1_ASM799701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:45,959] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:45,962] [INFO] Selected 10 target genomes.
[2024-01-24 14:29:45,962] [INFO] Target genome list was writen to GCF_007997015.1_ASM799701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:45,970] [INFO] Task started: fastANI
[2024-01-24 14:29:45,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae759c7-fcf5-4459-b798-12eaae42e0d5/GCF_007997015.1_ASM799701v1_genomic.fna.gz --refList GCF_007997015.1_ASM799701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007997015.1_ASM799701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:57,941] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:57,953] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:57,953] [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_007997015.1	s__Lujinxingia sp007997015	100.0	1816	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007997005.1	s__Lujinxingia sp007997005	89.8521	1591	1817	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	87.4057	1533	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	-
GCF_003260125.1	s__Lujinxingia litoralis	81.5859	1207	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697635.1	s__JACCWM01 sp013697635	76.8583	346	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258315.1	s__Bradymonas sediminis	76.6826	204	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Bradymonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006517175.1	s__Persicimonas caeni	76.6197	338	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007120035.1	s__SKON01 sp007120035	76.6037	275	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SKON01	95.0	99.72	99.66	0.90	0.87	5	-
GCA_007120615.1	s__SKNI01 sp007120615	75.8818	134	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SKNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119595.1	s__SLJM01 sp007119595	75.8539	111	1817	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SLJM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:57,990] [INFO] GTDB search result was written to GCF_007997015.1_ASM799701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:57,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:58,003] [INFO] DFAST_QC result json was written to GCF_007997015.1_ASM799701v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:58,004] [INFO] DFAST_QC completed!
[2024-01-24 14:29:58,004] [INFO] Total running time: 0h1m40s