[2024-01-25 19:01:35,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:35,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:35,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f4cf2dd-78d8-4e1b-bd33-86932abe9730/dqc_reference
[2024-01-25 19:01:36,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:36,862] [INFO] Task started: Prodigal
[2024-01-25 19:01:36,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg48e96c54-c0c4-4987-8cd5-a39397de0e57/GCF_014640115.1_ASM1464011v1_genomic.fna.gz | prodigal -d GCF_014640115.1_ASM1464011v1_genomic.fna/cds.fna -a GCF_014640115.1_ASM1464011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:47,759] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:47,759] [INFO] Task started: HMMsearch
[2024-01-25 19:01:47,759] [INFO] Running command: hmmsearch --tblout GCF_014640115.1_ASM1464011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f4cf2dd-78d8-4e1b-bd33-86932abe9730/dqc_reference/reference_markers.hmm GCF_014640115.1_ASM1464011v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:47,969] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:47,970] [INFO] Found 6/6 markers.
[2024-01-25 19:01:48,007] [INFO] Query marker FASTA was written to GCF_014640115.1_ASM1464011v1_genomic.fna/markers.fasta
[2024-01-25 19:01:48,007] [INFO] Task started: Blastn
[2024-01-25 19:01:48,007] [INFO] Running command: blastn -query GCF_014640115.1_ASM1464011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f4cf2dd-78d8-4e1b-bd33-86932abe9730/dqc_reference/reference_markers.fasta -out GCF_014640115.1_ASM1464011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:48,999] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:49,001] [INFO] Selected 27 target genomes.
[2024-01-25 19:01:49,001] [INFO] Target genome list was writen to GCF_014640115.1_ASM1464011v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:49,010] [INFO] Task started: fastANI
[2024-01-25 19:01:49,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e96c54-c0c4-4987-8cd5-a39397de0e57/GCF_014640115.1_ASM1464011v1_genomic.fna.gz --refList GCF_014640115.1_ASM1464011v1_genomic.fna/target_genomes.txt --output GCF_014640115.1_ASM1464011v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:10,198] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:10,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f4cf2dd-78d8-4e1b-bd33-86932abe9730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:10,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f4cf2dd-78d8-4e1b-bd33-86932abe9730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:10,214] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:02:10,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:02:10,215] [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
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	79.8193	581	1204	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.3291	497	1204	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	79.0716	436	1204	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	79.0338	442	1204	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.9579	519	1204	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	78.8502	506	1204	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	78.85	510	1204	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	78.8129	515	1204	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.7649	495	1204	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7478	435	1204	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.7254	463	1204	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.7249	441	1204	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.7154	473	1204	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.6793	445	1204	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	78.6778	453	1204	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	78.6415	471	1204	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.6332	442	1204	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.6309	505	1204	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.4725	450	1204	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	78.3503	392	1204	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.2532	392	1204	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.1613	361	1204	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.1302	354	1204	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.0595	371	1204	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.9765	350	1204	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.9149	416	1204	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.7377	338	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:10,216] [INFO] DFAST Taxonomy check result was written to GCF_014640115.1_ASM1464011v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:10,216] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:10,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:10,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f4cf2dd-78d8-4e1b-bd33-86932abe9730/dqc_reference/checkm_data
[2024-01-25 19:02:10,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:10,255] [INFO] Task started: CheckM
[2024-01-25 19:02:10,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640115.1_ASM1464011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640115.1_ASM1464011v1_genomic.fna/checkm_input GCF_014640115.1_ASM1464011v1_genomic.fna/checkm_result
[2024-01-25 19:02:48,605] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:48,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:48,621] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:48,621] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:48,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640115.1_ASM1464011v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:48,622] [INFO] Task started: Blastn
[2024-01-25 19:02:48,622] [INFO] Running command: blastn -query GCF_014640115.1_ASM1464011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f4cf2dd-78d8-4e1b-bd33-86932abe9730/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640115.1_ASM1464011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:50,629] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:50,633] [INFO] Selected 11 target genomes.
[2024-01-25 19:02:50,633] [INFO] Target genome list was writen to GCF_014640115.1_ASM1464011v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:50,645] [INFO] Task started: fastANI
[2024-01-25 19:02:50,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e96c54-c0c4-4987-8cd5-a39397de0e57/GCF_014640115.1_ASM1464011v1_genomic.fna.gz --refList GCF_014640115.1_ASM1464011v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640115.1_ASM1464011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:59,981] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:59,989] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:59,989] [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_014640115.1	s__Muriiphilus lacisalsi	100.0	1203	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900177545.1	s__Muriiphilus sp900177545	86.9285	913	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873585.1	s__Muriiphilus sp001873585	81.7127	408	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694465.1	s__Muriiphilus sp003694465	81.3309	340	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086115.1	s__Muriiphilus fusiformis	80.9212	682	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	98.34	98.34	0.92	0.92	2	-
GCA_002746935.1	s__Muriiphilus sp002746935	80.2003	498	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	79.8015	583	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.3803	491	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695005.1	s__Maritimibacter sp002695005	79.0863	526	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003344785.1	s__Puniceibacterium profundi	78.7545	456	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.6946	467	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:59,991] [INFO] GTDB search result was written to GCF_014640115.1_ASM1464011v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:59,991] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:59,994] [INFO] DFAST_QC result json was written to GCF_014640115.1_ASM1464011v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:59,995] [INFO] DFAST_QC completed!
[2024-01-25 19:02:59,995] [INFO] Total running time: 0h1m24s