[2024-01-24 11:12:39,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,890] [INFO] DQC Reference Directory: /var/lib/cwl/stgc65f6b1f-b6c4-4f3f-abe3-83ec8f45066a/dqc_reference
[2024-01-24 11:12:41,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,243] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg6043329a-1ff2-4db4-83b9-cbfba9a9330e/GCF_003217255.1_ASM321725v1_genomic.fna.gz | prodigal -d GCF_003217255.1_ASM321725v1_genomic.fna/cds.fna -a GCF_003217255.1_ASM321725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,358] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,359] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,359] [INFO] Running command: hmmsearch --tblout GCF_003217255.1_ASM321725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc65f6b1f-b6c4-4f3f-abe3-83ec8f45066a/dqc_reference/reference_markers.hmm GCF_003217255.1_ASM321725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:50,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:50,643] [INFO] Found 6/6 markers.
[2024-01-24 11:12:50,681] [INFO] Query marker FASTA was written to GCF_003217255.1_ASM321725v1_genomic.fna/markers.fasta
[2024-01-24 11:12:50,682] [INFO] Task started: Blastn
[2024-01-24 11:12:50,682] [INFO] Running command: blastn -query GCF_003217255.1_ASM321725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc65f6b1f-b6c4-4f3f-abe3-83ec8f45066a/dqc_reference/reference_markers.fasta -out GCF_003217255.1_ASM321725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:51,767] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:51,772] [INFO] Selected 22 target genomes.
[2024-01-24 11:12:51,772] [INFO] Target genome list was writen to GCF_003217255.1_ASM321725v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:51,782] [INFO] Task started: fastANI
[2024-01-24 11:12:51,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg6043329a-1ff2-4db4-83b9-cbfba9a9330e/GCF_003217255.1_ASM321725v1_genomic.fna.gz --refList GCF_003217255.1_ASM321725v1_genomic.fna/target_genomes.txt --output GCF_003217255.1_ASM321725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:09,050] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:09,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc65f6b1f-b6c4-4f3f-abe3-83ec8f45066a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:09,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc65f6b1f-b6c4-4f3f-abe3-83ec8f45066a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:09,068] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:09,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:09,068] [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
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	100.0	1133	1134	95	conclusive
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	80.7918	643	1134	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	80.1529	561	1134	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	80.116	555	1134	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	80.067	564	1134	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	79.8912	573	1134	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.6875	582	1134	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	79.6783	529	1134	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	79.6154	590	1134	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	79.6017	580	1134	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.6833	485	1134	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.6726	466	1134	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.5667	477	1134	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.5128	482	1134	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2434	364	1134	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1438	316	1134	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.9768	378	1134	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.9752	377	1134	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.9547	390	1134	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8616	334	1134	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.8356	438	1134	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.0582	294	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:09,070] [INFO] DFAST Taxonomy check result was written to GCF_003217255.1_ASM321725v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:09,071] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:09,071] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:09,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc65f6b1f-b6c4-4f3f-abe3-83ec8f45066a/dqc_reference/checkm_data
[2024-01-24 11:13:09,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:09,112] [INFO] Task started: CheckM
[2024-01-24 11:13:09,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217255.1_ASM321725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217255.1_ASM321725v1_genomic.fna/checkm_input GCF_003217255.1_ASM321725v1_genomic.fna/checkm_result
[2024-01-24 11:13:40,463] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:40,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:40,503] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:40,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:40,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217255.1_ASM321725v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:40,504] [INFO] Task started: Blastn
[2024-01-24 11:13:40,504] [INFO] Running command: blastn -query GCF_003217255.1_ASM321725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc65f6b1f-b6c4-4f3f-abe3-83ec8f45066a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217255.1_ASM321725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:42,653] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:42,658] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:42,658] [INFO] Target genome list was writen to GCF_003217255.1_ASM321725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:42,675] [INFO] Task started: fastANI
[2024-01-24 11:13:42,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg6043329a-1ff2-4db4-83b9-cbfba9a9330e/GCF_003217255.1_ASM321725v1_genomic.fna.gz --refList GCF_003217255.1_ASM321725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217255.1_ASM321725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:59,193] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:59,221] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:59,221] [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_003217255.1	s__Pseudoroseicyclus aestuarii	100.0	1133	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900102015.1	s__Limimaricola pyoseonensis	80.8018	643	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	80.4976	588	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	80.1483	561	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	80.0822	561	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900172345.1	s__Limimaricola soesokkakensis	79.9881	552	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900141735.1	s__Wenxinia saemankumensis	79.9001	572	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466965.1	s__Limimaricola cinnabarinus	79.6886	528	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	79.61	579	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.0602	445	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	78.6756	488	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCA_016806125.1	s__AWRV01 sp000504185	78.5566	455	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	78.5243	479	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017255395.1	s__AWRV01 sp017255395	78.4837	472	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	78.4347	298	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916275.1	s__Rubellimicrobium sp017916275	78.2515	387	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002166865.1	s__Roseovarius sp002166865	78.2473	327	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.2434	443	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	78.0534	273	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	77.9889	380	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:59,223] [INFO] GTDB search result was written to GCF_003217255.1_ASM321725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:59,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:59,228] [INFO] DFAST_QC result json was written to GCF_003217255.1_ASM321725v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:59,228] [INFO] DFAST_QC completed!
[2024-01-24 11:13:59,229] [INFO] Total running time: 0h1m19s