[2024-01-24 12:14:33,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c8ad58c-d64e-47fd-985e-47c76db997d1/dqc_reference
[2024-01-24 12:14:35,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,152] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg951b7c43-2157-465c-8447-10b3a102b986/GCF_014645075.1_ASM1464507v1_genomic.fna.gz | prodigal -d GCF_014645075.1_ASM1464507v1_genomic.fna/cds.fna -a GCF_014645075.1_ASM1464507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:45,190] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:45,191] [INFO] Task started: HMMsearch
[2024-01-24 12:14:45,191] [INFO] Running command: hmmsearch --tblout GCF_014645075.1_ASM1464507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c8ad58c-d64e-47fd-985e-47c76db997d1/dqc_reference/reference_markers.hmm GCF_014645075.1_ASM1464507v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:45,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:45,406] [INFO] Found 6/6 markers.
[2024-01-24 12:14:45,440] [INFO] Query marker FASTA was written to GCF_014645075.1_ASM1464507v1_genomic.fna/markers.fasta
[2024-01-24 12:14:45,440] [INFO] Task started: Blastn
[2024-01-24 12:14:45,440] [INFO] Running command: blastn -query GCF_014645075.1_ASM1464507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8ad58c-d64e-47fd-985e-47c76db997d1/dqc_reference/reference_markers.fasta -out GCF_014645075.1_ASM1464507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:46,382] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:46,385] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:46,385] [INFO] Target genome list was writen to GCF_014645075.1_ASM1464507v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:46,389] [INFO] Task started: fastANI
[2024-01-24 12:14:46,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg951b7c43-2157-465c-8447-10b3a102b986/GCF_014645075.1_ASM1464507v1_genomic.fna.gz --refList GCF_014645075.1_ASM1464507v1_genomic.fna/target_genomes.txt --output GCF_014645075.1_ASM1464507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:58,349] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:58,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c8ad58c-d64e-47fd-985e-47c76db997d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:58,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c8ad58c-d64e-47fd-985e-47c76db997d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:58,360] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:14:58,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:58,360] [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
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	100.0	1375	1376	95	conclusive
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	99.9913	1366	1376	95	conclusive
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	99.9797	1368	1376	95	conclusive
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	82.0766	784	1376	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	80.4948	667	1376	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	79.7147	542	1376	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.8355	570	1376	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	78.6531	487	1376	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.6273	499	1376	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.6257	485	1376	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9451	431	1376	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.8555	452	1376	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.1003	328	1376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:58,362] [INFO] DFAST Taxonomy check result was written to GCF_014645075.1_ASM1464507v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:58,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:58,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:58,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c8ad58c-d64e-47fd-985e-47c76db997d1/dqc_reference/checkm_data
[2024-01-24 12:14:58,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:58,404] [INFO] Task started: CheckM
[2024-01-24 12:14:58,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645075.1_ASM1464507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645075.1_ASM1464507v1_genomic.fna/checkm_input GCF_014645075.1_ASM1464507v1_genomic.fna/checkm_result
[2024-01-24 12:15:32,089] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:32,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:32,106] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:32,106] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:32,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645075.1_ASM1464507v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:32,107] [INFO] Task started: Blastn
[2024-01-24 12:15:32,107] [INFO] Running command: blastn -query GCF_014645075.1_ASM1464507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8ad58c-d64e-47fd-985e-47c76db997d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645075.1_ASM1464507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:33,844] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:33,846] [INFO] Selected 20 target genomes.
[2024-01-24 12:15:33,846] [INFO] Target genome list was writen to GCF_014645075.1_ASM1464507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:33,855] [INFO] Task started: fastANI
[2024-01-24 12:15:33,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg951b7c43-2157-465c-8447-10b3a102b986/GCF_014645075.1_ASM1464507v1_genomic.fna.gz --refList GCF_014645075.1_ASM1464507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645075.1_ASM1464507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:51,409] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:51,421] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:51,421] [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_000379485.1	s__Wenxinia marina	99.9913	1366	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_900141735.1	s__Wenxinia saemankumensis	82.068	784	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	80.5154	664	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	80.4427	703	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	79.7821	598	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	79.6665	559	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	79.6553	572	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	79.4494	578	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.182	623	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111315.1	s__Tranquillimonas rosea	79.0251	552	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.9217	575	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	78.8091	573	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	78.7871	513	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	78.7447	536	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172355.1	s__Oceanicola antarcticus	78.6826	593	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	78.6612	486	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	78.6332	469	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.4015	483	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	78.247	454	1376	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	77.9573	330	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:51,422] [INFO] GTDB search result was written to GCF_014645075.1_ASM1464507v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:51,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:51,426] [INFO] DFAST_QC result json was written to GCF_014645075.1_ASM1464507v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:51,427] [INFO] DFAST_QC completed!
[2024-01-24 12:15:51,427] [INFO] Total running time: 0h1m18s