[2024-01-24 11:50:48,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:48,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:48,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg049bfc27-e7c2-4834-afe1-eec7b7e330c8/dqc_reference
[2024-01-24 11:50:50,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,085] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgace0fba3-0b72-4751-993f-e6318c3b23aa/GCF_011682235.2_ASM1168223v2_genomic.fna.gz | prodigal -d GCF_011682235.2_ASM1168223v2_genomic.fna/cds.fna -a GCF_011682235.2_ASM1168223v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:16,331] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:16,331] [INFO] Task started: HMMsearch
[2024-01-24 11:51:16,331] [INFO] Running command: hmmsearch --tblout GCF_011682235.2_ASM1168223v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg049bfc27-e7c2-4834-afe1-eec7b7e330c8/dqc_reference/reference_markers.hmm GCF_011682235.2_ASM1168223v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:16,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:16,602] [INFO] Found 6/6 markers.
[2024-01-24 11:51:16,644] [INFO] Query marker FASTA was written to GCF_011682235.2_ASM1168223v2_genomic.fna/markers.fasta
[2024-01-24 11:51:16,645] [INFO] Task started: Blastn
[2024-01-24 11:51:16,645] [INFO] Running command: blastn -query GCF_011682235.2_ASM1168223v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg049bfc27-e7c2-4834-afe1-eec7b7e330c8/dqc_reference/reference_markers.fasta -out GCF_011682235.2_ASM1168223v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:17,305] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:17,310] [INFO] Selected 21 target genomes.
[2024-01-24 11:51:17,310] [INFO] Target genome list was writen to GCF_011682235.2_ASM1168223v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:17,323] [INFO] Task started: fastANI
[2024-01-24 11:51:17,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgace0fba3-0b72-4751-993f-e6318c3b23aa/GCF_011682235.2_ASM1168223v2_genomic.fna.gz --refList GCF_011682235.2_ASM1168223v2_genomic.fna/target_genomes.txt --output GCF_011682235.2_ASM1168223v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:32,228] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:32,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg049bfc27-e7c2-4834-afe1-eec7b7e330c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:32,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg049bfc27-e7c2-4834-afe1-eec7b7e330c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:32,246] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:32,247] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:32,247] [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
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	100.0	1500	1500	95	conclusive
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	76.4789	149	1500	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	76.4634	126	1500	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	76.4374	111	1500	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	76.3792	258	1500	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	76.2347	177	1500	95	below_threshold
Rhodothermus profundi	strain=DSM 22212	GCA_900142415.1	633813	633813	type	True	76.219	80	1500	95	below_threshold
Longimonas halophila	strain=KCTC 42399	GCA_002554705.1	1469170	1469170	type	True	75.9205	82	1500	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	75.3826	63	1500	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.2788	52	1500	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	75.2623	71	1500	95	below_threshold
Thermaurantiacus tibetensis	strain=SYSU G02173	GCA_015354055.1	2759035	2759035	type	True	75.1976	59	1500	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.1405	105	1500	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	74.9354	127	1500	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	74.9272	82	1500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:32,248] [INFO] DFAST Taxonomy check result was written to GCF_011682235.2_ASM1168223v2_genomic.fna/tc_result.tsv
[2024-01-24 11:51:32,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:32,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:32,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg049bfc27-e7c2-4834-afe1-eec7b7e330c8/dqc_reference/checkm_data
[2024-01-24 11:51:32,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:32,293] [INFO] Task started: CheckM
[2024-01-24 11:51:32,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011682235.2_ASM1168223v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011682235.2_ASM1168223v2_genomic.fna/checkm_input GCF_011682235.2_ASM1168223v2_genomic.fna/checkm_result
[2024-01-24 11:52:41,857] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:41,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:41,882] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:41,883] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:41,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011682235.2_ASM1168223v2_genomic.fna/markers.fasta)
[2024-01-24 11:52:41,884] [INFO] Task started: Blastn
[2024-01-24 11:52:41,884] [INFO] Running command: blastn -query GCF_011682235.2_ASM1168223v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg049bfc27-e7c2-4834-afe1-eec7b7e330c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_011682235.2_ASM1168223v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:42,810] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:42,814] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:42,814] [INFO] Target genome list was writen to GCF_011682235.2_ASM1168223v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:42,826] [INFO] Task started: fastANI
[2024-01-24 11:52:42,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgace0fba3-0b72-4751-993f-e6318c3b23aa/GCF_011682235.2_ASM1168223v2_genomic.fna.gz --refList GCF_011682235.2_ASM1168223v2_genomic.fna/target_genomes_gtdb.txt --output GCF_011682235.2_ASM1168223v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:52,207] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:52,217] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:52,217] [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
GCA_011682235.1	s__ISCAR-4553 sp011682235	99.9278	1401	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__ISCAR-4553;g__ISCAR-4553	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003285105.1	s__MEBICO9517 sp003285105	80.5697	562	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__MEBIC09517;g__MEBICO9517	95.0	96.96	96.85	0.95	0.94	3	-
GCF_000024845.1	s__Rhodothermus marinus	77.7946	316	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	95.50	95.42	0.92	0.91	8	-
GCA_009908885.1	s__JAAAOL01 sp009908885	77.4907	303	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487635.1	s__Rhodothermus sp015487635	77.3308	229	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	76.4942	236	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCF_002283365.1	s__Rubrivirga marina	76.3715	259	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643395.1	s__JABDJZ01 sp017643395	76.2665	169	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__UBA10348;g__JABDJZ01	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012269805.1	s__Rubrivirga sp012269805	76.2628	169	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	76.2146	179	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859335.1	s__JAAZVD01 sp017859335	75.88	69	1500	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__UBA10348;g__JAAZVD01	95.0	99.32	99.32	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:52,219] [INFO] GTDB search result was written to GCF_011682235.2_ASM1168223v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:52,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:52,223] [INFO] DFAST_QC result json was written to GCF_011682235.2_ASM1168223v2_genomic.fna/dqc_result.json
[2024-01-24 11:52:52,224] [INFO] DFAST_QC completed!
[2024-01-24 11:52:52,224] [INFO] Total running time: 0h2m3s