[2024-01-25 18:57:20,566] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:20,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:20,567] [INFO] DQC Reference Directory: /var/lib/cwl/stgf662465f-e34d-4002-9a31-a92ed0f6b912/dqc_reference
[2024-01-25 18:57:21,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:21,755] [INFO] Task started: Prodigal
[2024-01-25 18:57:21,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg26826c86-c30a-477f-b94c-3f556d07ed08/GCF_003340555.1_ASM334055v1_genomic.fna.gz | prodigal -d GCF_003340555.1_ASM334055v1_genomic.fna/cds.fna -a GCF_003340555.1_ASM334055v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:33,065] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:33,065] [INFO] Task started: HMMsearch
[2024-01-25 18:57:33,065] [INFO] Running command: hmmsearch --tblout GCF_003340555.1_ASM334055v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf662465f-e34d-4002-9a31-a92ed0f6b912/dqc_reference/reference_markers.hmm GCF_003340555.1_ASM334055v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:33,363] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:33,364] [INFO] Found 6/6 markers.
[2024-01-25 18:57:33,422] [INFO] Query marker FASTA was written to GCF_003340555.1_ASM334055v1_genomic.fna/markers.fasta
[2024-01-25 18:57:33,423] [INFO] Task started: Blastn
[2024-01-25 18:57:33,423] [INFO] Running command: blastn -query GCF_003340555.1_ASM334055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf662465f-e34d-4002-9a31-a92ed0f6b912/dqc_reference/reference_markers.fasta -out GCF_003340555.1_ASM334055v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:34,307] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:34,309] [INFO] Selected 14 target genomes.
[2024-01-25 18:57:34,310] [INFO] Target genome list was writen to GCF_003340555.1_ASM334055v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:34,327] [INFO] Task started: fastANI
[2024-01-25 18:57:34,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg26826c86-c30a-477f-b94c-3f556d07ed08/GCF_003340555.1_ASM334055v1_genomic.fna.gz --refList GCF_003340555.1_ASM334055v1_genomic.fna/target_genomes.txt --output GCF_003340555.1_ASM334055v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:46,806] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:46,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf662465f-e34d-4002-9a31-a92ed0f6b912/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:46,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf662465f-e34d-4002-9a31-a92ed0f6b912/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:46,816] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:46,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:46,817] [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 formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	100.0	1513	1518	95	conclusive
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	83.4205	1000	1518	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	83.4056	1002	1518	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	80.3406	720	1518	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	80.1239	662	1518	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	80.0328	666	1518	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	79.527	638	1518	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.9059	561	1518	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.67	450	1518	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4844	464	1518	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.3649	415	1518	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.3085	418	1518	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.2525	585	1518	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2457	468	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:46,818] [INFO] DFAST Taxonomy check result was written to GCF_003340555.1_ASM334055v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:46,819] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:46,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:46,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf662465f-e34d-4002-9a31-a92ed0f6b912/dqc_reference/checkm_data
[2024-01-25 18:57:46,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:46,865] [INFO] Task started: CheckM
[2024-01-25 18:57:46,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003340555.1_ASM334055v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003340555.1_ASM334055v1_genomic.fna/checkm_input GCF_003340555.1_ASM334055v1_genomic.fna/checkm_result
[2024-01-25 18:58:24,666] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:24,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:24,686] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:24,686] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:24,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003340555.1_ASM334055v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:24,687] [INFO] Task started: Blastn
[2024-01-25 18:58:24,687] [INFO] Running command: blastn -query GCF_003340555.1_ASM334055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf662465f-e34d-4002-9a31-a92ed0f6b912/dqc_reference/reference_markers_gtdb.fasta -out GCF_003340555.1_ASM334055v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:26,312] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:26,315] [INFO] Selected 11 target genomes.
[2024-01-25 18:58:26,315] [INFO] Target genome list was writen to GCF_003340555.1_ASM334055v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:26,325] [INFO] Task started: fastANI
[2024-01-25 18:58:26,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg26826c86-c30a-477f-b94c-3f556d07ed08/GCF_003340555.1_ASM334055v1_genomic.fna.gz --refList GCF_003340555.1_ASM334055v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003340555.1_ASM334055v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:36,252] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:36,260] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:36,261] [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_003340555.1	s__Jannaschia formosa	100.0	1513	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900116765.1	s__Jannaschia seohaensis	83.4214	1000	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013404595.1	s__Jannaschia marina	80.3647	717	1518	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	80.0001	670	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016820245.1	s__Jannaschia sp016820245	79.9813	706	1518	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	79.7616	566	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	79.5382	637	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.8559	568	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	78.5289	459	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	78.3526	336	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.2459	586	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:36,262] [INFO] GTDB search result was written to GCF_003340555.1_ASM334055v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:36,263] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:36,265] [INFO] DFAST_QC result json was written to GCF_003340555.1_ASM334055v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:36,266] [INFO] DFAST_QC completed!
[2024-01-25 18:58:36,266] [INFO] Total running time: 0h1m16s