[2024-01-25 20:03:35,424] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:35,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:35,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg12f146fd-72d9-4347-bb1f-48551116f984/dqc_reference
[2024-01-25 20:03:36,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:36,551] [INFO] Task started: Prodigal
[2024-01-25 20:03:36,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg9095e354-0507-4298-a2c1-88ceb89b7281/GCF_015679265.1_ASM1567926v1_genomic.fna.gz | prodigal -d GCF_015679265.1_ASM1567926v1_genomic.fna/cds.fna -a GCF_015679265.1_ASM1567926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:47,418] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:47,419] [INFO] Task started: HMMsearch
[2024-01-25 20:03:47,419] [INFO] Running command: hmmsearch --tblout GCF_015679265.1_ASM1567926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12f146fd-72d9-4347-bb1f-48551116f984/dqc_reference/reference_markers.hmm GCF_015679265.1_ASM1567926v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:47,673] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:47,674] [INFO] Found 6/6 markers.
[2024-01-25 20:03:47,709] [INFO] Query marker FASTA was written to GCF_015679265.1_ASM1567926v1_genomic.fna/markers.fasta
[2024-01-25 20:03:47,710] [INFO] Task started: Blastn
[2024-01-25 20:03:47,710] [INFO] Running command: blastn -query GCF_015679265.1_ASM1567926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12f146fd-72d9-4347-bb1f-48551116f984/dqc_reference/reference_markers.fasta -out GCF_015679265.1_ASM1567926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:48,657] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:48,659] [INFO] Selected 24 target genomes.
[2024-01-25 20:03:48,660] [INFO] Target genome list was writen to GCF_015679265.1_ASM1567926v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:48,685] [INFO] Task started: fastANI
[2024-01-25 20:03:48,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg9095e354-0507-4298-a2c1-88ceb89b7281/GCF_015679265.1_ASM1567926v1_genomic.fna.gz --refList GCF_015679265.1_ASM1567926v1_genomic.fna/target_genomes.txt --output GCF_015679265.1_ASM1567926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:08,528] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:08,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12f146fd-72d9-4347-bb1f-48551116f984/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:08,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12f146fd-72d9-4347-bb1f-48551116f984/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:08,542] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:08,543] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:08,543] [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
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	100.0	1398	1399	95	conclusive
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.1681	407	1399	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	78.0873	384	1399	95	below_threshold
Pontivivens insulae	strain=CeCT 8812	GCA_900302495.1	1639689	1639689	type	True	78.0868	341	1399	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	78.0725	383	1399	95	below_threshold
Pontivivens insulae	strain=DSM 103361	GCA_003385715.1	1639689	1639689	type	True	78.061	341	1399	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.929	447	1399	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.9203	419	1399	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.9057	410	1399	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.8853	403	1399	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	77.7806	389	1399	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	77.774	389	1399	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	77.7367	366	1399	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.7232	350	1399	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.5745	350	1399	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.5526	340	1399	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	77.3401	329	1399	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	77.3388	302	1399	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.3222	347	1399	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.2741	318	1399	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	77.2518	314	1399	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.2164	332	1399	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	77.1021	284	1399	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	76.5284	224	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:08,544] [INFO] DFAST Taxonomy check result was written to GCF_015679265.1_ASM1567926v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:08,545] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:08,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:08,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12f146fd-72d9-4347-bb1f-48551116f984/dqc_reference/checkm_data
[2024-01-25 20:04:08,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:08,590] [INFO] Task started: CheckM
[2024-01-25 20:04:08,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015679265.1_ASM1567926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015679265.1_ASM1567926v1_genomic.fna/checkm_input GCF_015679265.1_ASM1567926v1_genomic.fna/checkm_result
[2024-01-25 20:04:44,798] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:44,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:44,816] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:44,817] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:44,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015679265.1_ASM1567926v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:44,817] [INFO] Task started: Blastn
[2024-01-25 20:04:44,817] [INFO] Running command: blastn -query GCF_015679265.1_ASM1567926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12f146fd-72d9-4347-bb1f-48551116f984/dqc_reference/reference_markers_gtdb.fasta -out GCF_015679265.1_ASM1567926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:46,686] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:46,688] [INFO] Selected 22 target genomes.
[2024-01-25 20:04:46,689] [INFO] Target genome list was writen to GCF_015679265.1_ASM1567926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:46,715] [INFO] Task started: fastANI
[2024-01-25 20:04:46,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg9095e354-0507-4298-a2c1-88ceb89b7281/GCF_015679265.1_ASM1567926v1_genomic.fna.gz --refList GCF_015679265.1_ASM1567926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015679265.1_ASM1567926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:04,684] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:04,697] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:04,697] [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_015679265.1	s__MT2928 sp015679265	100.0	1399	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011290545.1	s__Monaibacterium sp011290545	78.572	438	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	96.75	96.75	0.88	0.88	2	-
GCF_003448965.1	s__Paroceanicella sp003448965	78.2863	481	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	78.2448	428	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.1733	464	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070395.1	s__CLL3-39 sp012070395	78.1026	384	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CLL3-39	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900302495.1	s__Pontivivens insulae	78.0868	341	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontivivens	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000521865.1	s__Roseivivax isoporae	77.9842	440	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.9583	397	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.9149	409	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116765.1	s__Jannaschia seohaensis	77.773	390	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900106695.1	s__Albimonas donghaensis	77.6293	447	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.6009	448	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	77.5961	377	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_017995835.1	s__Amaricoccus sp017995835	77.485	326	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	77.4632	335	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900231835.1	s__Monaibacterium marinum	77.3984	285	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	77.367	317	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCF_002797755.1	s__Brevirhabdus pacifica	77.3614	320	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_003709565.1	s__Paracoccus siganidrum	77.2823	351	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003054285.1	s__Litoreibacter ponti	77.2523	314	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199445.1	s__Rubricella aquisinus	76.9542	292	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubricella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:04,699] [INFO] GTDB search result was written to GCF_015679265.1_ASM1567926v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:04,699] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:04,703] [INFO] DFAST_QC result json was written to GCF_015679265.1_ASM1567926v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:04,704] [INFO] DFAST_QC completed!
[2024-01-25 20:05:04,704] [INFO] Total running time: 0h1m29s