[2024-01-24 11:59:51,989] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,991] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg3191c360-fe43-448d-82f0-216a22464580/dqc_reference
[2024-01-24 11:59:55,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,381] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,381] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9ba962d-4a22-4a22-967d-e11f0dbce1b3/GCF_003149265.1_ASM314926v1_genomic.fna.gz | prodigal -d GCF_003149265.1_ASM314926v1_genomic.fna/cds.fna -a GCF_003149265.1_ASM314926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:08,872] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:08,873] [INFO] Task started: HMMsearch
[2024-01-24 12:00:08,873] [INFO] Running command: hmmsearch --tblout GCF_003149265.1_ASM314926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3191c360-fe43-448d-82f0-216a22464580/dqc_reference/reference_markers.hmm GCF_003149265.1_ASM314926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:09,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:09,154] [INFO] Found 6/6 markers.
[2024-01-24 12:00:09,204] [INFO] Query marker FASTA was written to GCF_003149265.1_ASM314926v1_genomic.fna/markers.fasta
[2024-01-24 12:00:09,204] [INFO] Task started: Blastn
[2024-01-24 12:00:09,205] [INFO] Running command: blastn -query GCF_003149265.1_ASM314926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3191c360-fe43-448d-82f0-216a22464580/dqc_reference/reference_markers.fasta -out GCF_003149265.1_ASM314926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:10,137] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:10,141] [INFO] Selected 17 target genomes.
[2024-01-24 12:00:10,142] [INFO] Target genome list was writen to GCF_003149265.1_ASM314926v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:10,149] [INFO] Task started: fastANI
[2024-01-24 12:00:10,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ba962d-4a22-4a22-967d-e11f0dbce1b3/GCF_003149265.1_ASM314926v1_genomic.fna.gz --refList GCF_003149265.1_ASM314926v1_genomic.fna/target_genomes.txt --output GCF_003149265.1_ASM314926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:23,633] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:23,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3191c360-fe43-448d-82f0-216a22464580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:23,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3191c360-fe43-448d-82f0-216a22464580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:23,652] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:00:23,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:23,653] [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
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	100.0	1594	1594	95	conclusive
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	100.0	1594	1594	95	conclusive
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	83.4586	987	1594	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	79.5267	637	1594	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.1902	560	1594	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.1746	561	1594	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	79.1365	591	1594	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.3023	451	1594	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2555	423	1594	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2049	401	1594	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.1852	396	1594	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.9852	386	1594	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.9584	352	1594	95	below_threshold
Jannaschia faecimaris	strain=DSM 100420	GCA_900107415.1	1244108	1244108	type	True	77.8136	448	1594	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.8015	385	1594	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6897	353	1594	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.2896	435	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:23,655] [INFO] DFAST Taxonomy check result was written to GCF_003149265.1_ASM314926v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:23,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:23,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:23,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3191c360-fe43-448d-82f0-216a22464580/dqc_reference/checkm_data
[2024-01-24 12:00:23,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:23,702] [INFO] Task started: CheckM
[2024-01-24 12:00:23,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149265.1_ASM314926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149265.1_ASM314926v1_genomic.fna/checkm_input GCF_003149265.1_ASM314926v1_genomic.fna/checkm_result
[2024-01-24 12:01:05,426] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:05,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:05,452] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:05,452] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:05,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149265.1_ASM314926v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:05,453] [INFO] Task started: Blastn
[2024-01-24 12:01:05,453] [INFO] Running command: blastn -query GCF_003149265.1_ASM314926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3191c360-fe43-448d-82f0-216a22464580/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149265.1_ASM314926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:07,198] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:07,203] [INFO] Selected 13 target genomes.
[2024-01-24 12:01:07,203] [INFO] Target genome list was writen to GCF_003149265.1_ASM314926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:07,213] [INFO] Task started: fastANI
[2024-01-24 12:01:07,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ba962d-4a22-4a22-967d-e11f0dbce1b3/GCF_003149265.1_ASM314926v1_genomic.fna.gz --refList GCF_003149265.1_ASM314926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149265.1_ASM314926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:18,550] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:18,566] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:18,567] [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_900116765.1	s__Jannaschia seohaensis	100.0	1594	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003340555.1	s__Jannaschia formosa	83.4404	989	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	79.5096	641	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	79.3144	504	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820245.1	s__Jannaschia sp016820245	79.2196	577	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.1956	560	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113875.1	s__Jannaschia pohangensis	79.1126	594	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000877395.1	s__Jannaschia aquimarina	79.0148	527	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.2848	453	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	78.1518	516	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.9522	352	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107415.1	s__Jannaschia faecimaris	77.8136	448	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.6831	528	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:18,568] [INFO] GTDB search result was written to GCF_003149265.1_ASM314926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:18,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:18,575] [INFO] DFAST_QC result json was written to GCF_003149265.1_ASM314926v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:18,575] [INFO] DFAST_QC completed!
[2024-01-24 12:01:18,576] [INFO] Total running time: 0h1m27s