[2024-01-25 18:37:35,686] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:35,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:35,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7323cc1-6cb7-40cf-893e-83750710289e/dqc_reference
[2024-01-25 18:37:36,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:36,901] [INFO] Task started: Prodigal
[2024-01-25 18:37:36,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg7038f6fb-415f-4e96-912a-c6331bc7dbba/GCF_004005565.1_ASM400556v1_genomic.fna.gz | prodigal -d GCF_004005565.1_ASM400556v1_genomic.fna/cds.fna -a GCF_004005565.1_ASM400556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:52,086] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:52,086] [INFO] Task started: HMMsearch
[2024-01-25 18:37:52,086] [INFO] Running command: hmmsearch --tblout GCF_004005565.1_ASM400556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7323cc1-6cb7-40cf-893e-83750710289e/dqc_reference/reference_markers.hmm GCF_004005565.1_ASM400556v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:52,397] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:52,398] [INFO] Found 6/6 markers.
[2024-01-25 18:37:52,439] [INFO] Query marker FASTA was written to GCF_004005565.1_ASM400556v1_genomic.fna/markers.fasta
[2024-01-25 18:37:52,439] [INFO] Task started: Blastn
[2024-01-25 18:37:52,439] [INFO] Running command: blastn -query GCF_004005565.1_ASM400556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7323cc1-6cb7-40cf-893e-83750710289e/dqc_reference/reference_markers.fasta -out GCF_004005565.1_ASM400556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:53,061] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:53,064] [INFO] Selected 23 target genomes.
[2024-01-25 18:37:53,064] [INFO] Target genome list was writen to GCF_004005565.1_ASM400556v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:53,082] [INFO] Task started: fastANI
[2024-01-25 18:37:53,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg7038f6fb-415f-4e96-912a-c6331bc7dbba/GCF_004005565.1_ASM400556v1_genomic.fna.gz --refList GCF_004005565.1_ASM400556v1_genomic.fna/target_genomes.txt --output GCF_004005565.1_ASM400556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:38:12,992] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:12,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7323cc1-6cb7-40cf-893e-83750710289e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:38:12,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7323cc1-6cb7-40cf-893e-83750710289e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:38:13,003] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:38:13,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:38:13,003] [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 sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	100.0	1753	1754	95	conclusive
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	87.3627	1547	1754	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	82.4671	1167	1754	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	76.4692	255	1754	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	76.4631	256	1754	95	below_threshold
Bradymonas sediminis	strain=DSM 28820	GCA_004362595.1	1548548	1548548	type	True	76.2687	169	1754	95	below_threshold
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	76.2678	169	1754	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	75.1899	67	1754	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.1173	55	1754	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	75.1101	73	1754	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	75.0663	67	1754	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	74.9763	53	1754	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	74.9523	64	1754	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.9457	98	1754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:38:13,005] [INFO] DFAST Taxonomy check result was written to GCF_004005565.1_ASM400556v1_genomic.fna/tc_result.tsv
[2024-01-25 18:38:13,005] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:38:13,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:38:13,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7323cc1-6cb7-40cf-893e-83750710289e/dqc_reference/checkm_data
[2024-01-25 18:38:13,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:38:13,057] [INFO] Task started: CheckM
[2024-01-25 18:38:13,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005565.1_ASM400556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005565.1_ASM400556v1_genomic.fna/checkm_input GCF_004005565.1_ASM400556v1_genomic.fna/checkm_result
[2024-01-25 18:38:57,351] [INFO] Task succeeded: CheckM
[2024-01-25 18:38:57,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:38:57,375] [INFO] ===== Completeness check finished =====
[2024-01-25 18:38:57,376] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:38:57,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005565.1_ASM400556v1_genomic.fna/markers.fasta)
[2024-01-25 18:38:57,376] [INFO] Task started: Blastn
[2024-01-25 18:38:57,376] [INFO] Running command: blastn -query GCF_004005565.1_ASM400556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7323cc1-6cb7-40cf-893e-83750710289e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005565.1_ASM400556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:58,448] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:58,451] [INFO] Selected 8 target genomes.
[2024-01-25 18:38:58,451] [INFO] Target genome list was writen to GCF_004005565.1_ASM400556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:38:58,479] [INFO] Task started: fastANI
[2024-01-25 18:38:58,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg7038f6fb-415f-4e96-912a-c6331bc7dbba/GCF_004005565.1_ASM400556v1_genomic.fna.gz --refList GCF_004005565.1_ASM400556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005565.1_ASM400556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:39:09,800] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:09,807] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:39:09,807] [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_004005565.1	s__Lujinxingia sediminis	100.0	1753	1754	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	conclusive
GCA_007997005.1	s__Lujinxingia sp007997005	88.4118	1538	1754	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007997015.1	s__Lujinxingia sp007997015	87.3632	1547	1754	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	82.458	1168	1754	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120035.1	s__SKON01 sp007120035	76.5822	237	1754	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SKON01	95.0	99.72	99.66	0.90	0.87	5	-
GCA_013697635.1	s__JACCWM01 sp013697635	76.4873	285	1754	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517175.1	s__Persicimonas caeni	76.4611	256	1754	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007119595.1	s__SLJM01 sp007119595	75.7479	85	1754	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SLJM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:39:09,811] [INFO] GTDB search result was written to GCF_004005565.1_ASM400556v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:39:09,811] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:39:09,816] [INFO] DFAST_QC result json was written to GCF_004005565.1_ASM400556v1_genomic.fna/dqc_result.json
[2024-01-25 18:39:09,816] [INFO] DFAST_QC completed!
[2024-01-25 18:39:09,816] [INFO] Total running time: 0h1m34s