[2024-01-24 12:54:05,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg08ec80db-0ed2-4ac4-a144-0e74ba570f1e/dqc_reference
[2024-01-24 12:54:07,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,744] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,748] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa8ae0d6-edeb-4d6b-9dac-196322d1a500/GCF_008079445.1_ASM807944v1_genomic.fna.gz | prodigal -d GCF_008079445.1_ASM807944v1_genomic.fna/cds.fna -a GCF_008079445.1_ASM807944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:20,243] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:20,244] [INFO] Task started: HMMsearch
[2024-01-24 12:54:20,244] [INFO] Running command: hmmsearch --tblout GCF_008079445.1_ASM807944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08ec80db-0ed2-4ac4-a144-0e74ba570f1e/dqc_reference/reference_markers.hmm GCF_008079445.1_ASM807944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:20,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:20,612] [INFO] Found 6/6 markers.
[2024-01-24 12:54:20,648] [INFO] Query marker FASTA was written to GCF_008079445.1_ASM807944v1_genomic.fna/markers.fasta
[2024-01-24 12:54:20,649] [INFO] Task started: Blastn
[2024-01-24 12:54:20,649] [INFO] Running command: blastn -query GCF_008079445.1_ASM807944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08ec80db-0ed2-4ac4-a144-0e74ba570f1e/dqc_reference/reference_markers.fasta -out GCF_008079445.1_ASM807944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:21,467] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:21,470] [INFO] Selected 22 target genomes.
[2024-01-24 12:54:21,471] [INFO] Target genome list was writen to GCF_008079445.1_ASM807944v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:21,491] [INFO] Task started: fastANI
[2024-01-24 12:54:21,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8ae0d6-edeb-4d6b-9dac-196322d1a500/GCF_008079445.1_ASM807944v1_genomic.fna.gz --refList GCF_008079445.1_ASM807944v1_genomic.fna/target_genomes.txt --output GCF_008079445.1_ASM807944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:37,998] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:37,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08ec80db-0ed2-4ac4-a144-0e74ba570f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:38,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08ec80db-0ed2-4ac4-a144-0e74ba570f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:38,021] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:38,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:38,022] [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
Aidingimonas lacisalsi	strain=XHU 5135	GCA_008079445.1	2604086	2604086	type	True	100.0	1303	1307	95	conclusive
Aidingimonas halophila	strain=KCTC 12885	GCA_014651655.1	574349	574349	type	True	83.3595	811	1307	95	below_threshold
Aidingimonas halophila	strain=DSM 19219	GCA_900106955.1	574349	574349	type	True	83.2171	829	1307	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	78.257	302	1307	95	below_threshold
Halomonas qijiaojingensis	strain=KCTC 22228	GCA_014651875.1	980347	980347	type	True	78.2342	351	1307	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	78.0593	262	1307	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.0222	268	1307	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	77.9787	284	1307	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	77.9682	322	1307	95	below_threshold
Halomonas anticariensis	strain=FP35	GCA_000409775.1	258591	258591	type	True	77.9078	364	1307	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	77.8637	297	1307	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	77.8557	236	1307	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	77.8276	265	1307	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.7712	265	1307	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	77.7607	215	1307	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	77.7156	244	1307	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.6985	277	1307	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.5612	255	1307	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	77.4279	182	1307	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	77.3756	177	1307	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	77.0819	156	1307	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	77.0325	159	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:38,024] [INFO] DFAST Taxonomy check result was written to GCF_008079445.1_ASM807944v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:38,024] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:38,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:38,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08ec80db-0ed2-4ac4-a144-0e74ba570f1e/dqc_reference/checkm_data
[2024-01-24 12:54:38,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:38,069] [INFO] Task started: CheckM
[2024-01-24 12:54:38,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008079445.1_ASM807944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008079445.1_ASM807944v1_genomic.fna/checkm_input GCF_008079445.1_ASM807944v1_genomic.fna/checkm_result
[2024-01-24 12:55:19,169] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:19,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:19,193] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:19,194] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:19,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008079445.1_ASM807944v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:19,195] [INFO] Task started: Blastn
[2024-01-24 12:55:19,195] [INFO] Running command: blastn -query GCF_008079445.1_ASM807944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08ec80db-0ed2-4ac4-a144-0e74ba570f1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_008079445.1_ASM807944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:20,513] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:20,517] [INFO] Selected 23 target genomes.
[2024-01-24 12:55:20,517] [INFO] Target genome list was writen to GCF_008079445.1_ASM807944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:20,544] [INFO] Task started: fastANI
[2024-01-24 12:55:20,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8ae0d6-edeb-4d6b-9dac-196322d1a500/GCF_008079445.1_ASM807944v1_genomic.fna.gz --refList GCF_008079445.1_ASM807944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008079445.1_ASM807944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:35,933] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:35,956] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:35,957] [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_008079445.1	s__Aidingimonas lacisalsi	100.0	1303	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Aidingimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106955.1	s__Aidingimonas halophila	83.2171	829	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Aidingimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014192275.1	s__Halomonas stenophila	78.252	303	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651875.1	s__Halomonas_A qijiaojingensis	78.2234	352	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014840935.1	s__Halomonas_E sp014840935	78.0768	275	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	78.0756	246	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	78.0524	262	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977575.1	s__Halomonas_B socia	78.044	368	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	77.9902	283	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_900128925.1	s__Halomonas_C ilicicola	77.9712	255	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102875.1	s__Halomonas_B pantelleriensis	77.9682	322	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192215.1	s__Halomonas cerina	77.9008	264	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009902005.1	s__Halomonas alimentaria	77.8468	236	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100755.1	s__Halomonas_E taeanensis	77.815	266	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	98.15	98.15	0.92	0.92	2	-
GCF_003056305.1	s__Halomonas denitrificans	77.7479	279	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116405.1	s__Halomonas saccharevitans	77.7393	243	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	77.5843	194	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902500215.1	s__Halomonas sp902500215	77.5645	254	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993675.1	s__Halomonas_C sp010993675	77.5245	266	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001937195.1	s__Salinicola socius	77.3762	177	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_012427705.1	s__Halomonas piezotolerans	77.0797	157	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_009846525.1	s__Halomonas sp002696125	77.0038	126	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:35,959] [INFO] GTDB search result was written to GCF_008079445.1_ASM807944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:35,961] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:35,966] [INFO] DFAST_QC result json was written to GCF_008079445.1_ASM807944v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:35,967] [INFO] DFAST_QC completed!
[2024-01-24 12:55:35,967] [INFO] Total running time: 0h1m31s