[2024-01-24 14:05:36,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfc9a04c-1021-434a-92f8-189f5deb2b36/dqc_reference
[2024-01-24 14:05:37,966] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,967] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,967] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb9472c2-6c15-42ed-a08b-8289c2b6fdb6/GCF_002869745.1_ASM286974v1_genomic.fna.gz | prodigal -d GCF_002869745.1_ASM286974v1_genomic.fna/cds.fna -a GCF_002869745.1_ASM286974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:49,801] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:49,802] [INFO] Task started: HMMsearch
[2024-01-24 14:05:49,802] [INFO] Running command: hmmsearch --tblout GCF_002869745.1_ASM286974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfc9a04c-1021-434a-92f8-189f5deb2b36/dqc_reference/reference_markers.hmm GCF_002869745.1_ASM286974v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:50,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:50,147] [INFO] Found 6/6 markers.
[2024-01-24 14:05:50,205] [INFO] Query marker FASTA was written to GCF_002869745.1_ASM286974v1_genomic.fna/markers.fasta
[2024-01-24 14:05:50,206] [INFO] Task started: Blastn
[2024-01-24 14:05:50,206] [INFO] Running command: blastn -query GCF_002869745.1_ASM286974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc9a04c-1021-434a-92f8-189f5deb2b36/dqc_reference/reference_markers.fasta -out GCF_002869745.1_ASM286974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:51,173] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:51,178] [INFO] Selected 29 target genomes.
[2024-01-24 14:05:51,178] [INFO] Target genome list was writen to GCF_002869745.1_ASM286974v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:51,189] [INFO] Task started: fastANI
[2024-01-24 14:05:51,190] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9472c2-6c15-42ed-a08b-8289c2b6fdb6/GCF_002869745.1_ASM286974v1_genomic.fna.gz --refList GCF_002869745.1_ASM286974v1_genomic.fna/target_genomes.txt --output GCF_002869745.1_ASM286974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:15,068] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:15,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfc9a04c-1021-434a-92f8-189f5deb2b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:15,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfc9a04c-1021-434a-92f8-189f5deb2b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:15,092] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:15,092] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:15,092] [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
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	79.8746	689	1424	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.6911	635	1424	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.6294	637	1424	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	79.5306	628	1424	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.5079	639	1424	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	79.4839	627	1424	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.3636	636	1424	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.3459	634	1424	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	79.1695	487	1424	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.0579	650	1424	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	79.0485	554	1424	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	79.0069	568	1424	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.9358	618	1424	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	78.8907	522	1424	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.8704	560	1424	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8683	511	1424	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.862	551	1424	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.8136	604	1424	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	78.7949	555	1424	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.7642	507	1424	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.6452	527	1424	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.6417	526	1424	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.6327	567	1424	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.6043	514	1424	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.556	530	1424	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.543	488	1424	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	78.4937	538	1424	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1005	414	1424	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.5116	396	1424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:15,094] [INFO] DFAST Taxonomy check result was written to GCF_002869745.1_ASM286974v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:15,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:15,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:15,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfc9a04c-1021-434a-92f8-189f5deb2b36/dqc_reference/checkm_data
[2024-01-24 14:06:15,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:15,140] [INFO] Task started: CheckM
[2024-01-24 14:06:15,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002869745.1_ASM286974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002869745.1_ASM286974v1_genomic.fna/checkm_input GCF_002869745.1_ASM286974v1_genomic.fna/checkm_result
[2024-01-24 14:06:57,684] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:57,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:57,707] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:57,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:57,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002869745.1_ASM286974v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:57,708] [INFO] Task started: Blastn
[2024-01-24 14:06:57,709] [INFO] Running command: blastn -query GCF_002869745.1_ASM286974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc9a04c-1021-434a-92f8-189f5deb2b36/dqc_reference/reference_markers_gtdb.fasta -out GCF_002869745.1_ASM286974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:59,395] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:59,399] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:59,400] [INFO] Target genome list was writen to GCF_002869745.1_ASM286974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:59,428] [INFO] Task started: fastANI
[2024-01-24 14:06:59,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9472c2-6c15-42ed-a08b-8289c2b6fdb6/GCF_002869745.1_ASM286974v1_genomic.fna.gz --refList GCF_002869745.1_ASM286974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002869745.1_ASM286974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:19,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,919] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:19,919] [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_002869745.1	s__Oceaniglobus roseus	100.0	1418	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115595.1	s__Tranquillimonas alkanivorans	80.1581	632	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002751875.1	s__Oceaniglobus indicus	80.0114	684	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.6676	608	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	79.6383	686	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.6312	636	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	79.3863	563	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.2132	615	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	79.1851	643	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	79.1509	582	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	79.0781	551	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	79.0227	567	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	78.9642	565	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.8457	586	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	78.745	553	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_009835145.1	s__Profundibacterium mesophilum	78.698	484	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	78.6397	480	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	78.6394	566	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_003054175.1	s__Allosediminivita pacifica	78.621	528	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000743715.1	s__Palleronia rufa	78.5991	511	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.5437	488	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	78.3532	437	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973535.1	s__Albidovulum denitrificans	78.2412	488	1424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:19,922] [INFO] GTDB search result was written to GCF_002869745.1_ASM286974v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:19,922] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:19,927] [INFO] DFAST_QC result json was written to GCF_002869745.1_ASM286974v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:19,927] [INFO] DFAST_QC completed!
[2024-01-24 14:07:19,927] [INFO] Total running time: 0h1m43s