[2024-01-24 13:32:16,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:16,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:16,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg90e4ad1e-9aaa-4b28-9e04-894fa12558a6/dqc_reference
[2024-01-24 13:32:18,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:18,340] [INFO] Task started: Prodigal
[2024-01-24 13:32:18,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg722c484f-d714-4e67-940b-19e305fbe3c7/GCF_014651655.1_ASM1465165v1_genomic.fna.gz | prodigal -d GCF_014651655.1_ASM1465165v1_genomic.fna/cds.fna -a GCF_014651655.1_ASM1465165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:30,639] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:30,640] [INFO] Task started: HMMsearch
[2024-01-24 13:32:30,640] [INFO] Running command: hmmsearch --tblout GCF_014651655.1_ASM1465165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90e4ad1e-9aaa-4b28-9e04-894fa12558a6/dqc_reference/reference_markers.hmm GCF_014651655.1_ASM1465165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:30,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:30,902] [INFO] Found 6/6 markers.
[2024-01-24 13:32:30,941] [INFO] Query marker FASTA was written to GCF_014651655.1_ASM1465165v1_genomic.fna/markers.fasta
[2024-01-24 13:32:30,941] [INFO] Task started: Blastn
[2024-01-24 13:32:30,941] [INFO] Running command: blastn -query GCF_014651655.1_ASM1465165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e4ad1e-9aaa-4b28-9e04-894fa12558a6/dqc_reference/reference_markers.fasta -out GCF_014651655.1_ASM1465165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:31,696] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:31,700] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:31,700] [INFO] Target genome list was writen to GCF_014651655.1_ASM1465165v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:31,710] [INFO] Task started: fastANI
[2024-01-24 13:32:31,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg722c484f-d714-4e67-940b-19e305fbe3c7/GCF_014651655.1_ASM1465165v1_genomic.fna.gz --refList GCF_014651655.1_ASM1465165v1_genomic.fna/target_genomes.txt --output GCF_014651655.1_ASM1465165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:52,835] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:52,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90e4ad1e-9aaa-4b28-9e04-894fa12558a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:52,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90e4ad1e-9aaa-4b28-9e04-894fa12558a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:52,855] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:52,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:52,855] [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 halophila	strain=KCTC 12885	GCA_014651655.1	574349	574349	type	True	100.0	1274	1277	95	conclusive
Aidingimonas halophila	strain=DSM 19219	GCA_900106955.1	574349	574349	type	True	99.9979	1274	1277	95	conclusive
Aidingimonas lacisalsi	strain=XHU 5135	GCA_008079445.1	2604086	2604086	type	True	83.1434	825	1277	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	78.2205	302	1277	95	below_threshold
Halomonas qijiaojingensis	strain=KCTC 22228	GCA_014651875.1	980347	980347	type	True	78.1918	373	1277	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	78.0546	286	1277	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	77.9037	273	1277	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.8909	268	1277	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	77.8614	305	1277	95	below_threshold
Halomonas anticariensis	strain=DSM 16096	GCA_000428505.1	258591	258591	type	True	77.7956	352	1277	95	below_threshold
Halomonas anticariensis	strain=FP35	GCA_000409775.1	258591	258591	type	True	77.7904	364	1277	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.7642	303	1277	95	below_threshold
Halomonas fontilapidosi	strain=CECT 7341	GCA_014192285.1	616675	616675	type	True	77.7614	281	1277	95	below_threshold
Halomonas pellis	strain=L5	GCA_008297955.1	2606936	2606936	type	True	77.7556	279	1277	95	below_threshold
Halomonas xianhensis	strain=CGMCC 1.6848	GCA_900113605.1	442341	442341	type	True	77.7428	272	1277	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.7197	275	1277	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	77.6993	253	1277	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	77.6577	307	1277	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.5692	272	1277	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.5074	297	1277	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	77.4834	255	1277	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	77.4584	117	1277	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	77.3372	118	1277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:52,857] [INFO] DFAST Taxonomy check result was written to GCF_014651655.1_ASM1465165v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:52,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:52,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:52,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90e4ad1e-9aaa-4b28-9e04-894fa12558a6/dqc_reference/checkm_data
[2024-01-24 13:32:52,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:52,907] [INFO] Task started: CheckM
[2024-01-24 13:32:52,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651655.1_ASM1465165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651655.1_ASM1465165v1_genomic.fna/checkm_input GCF_014651655.1_ASM1465165v1_genomic.fna/checkm_result
[2024-01-24 13:33:34,947] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:34,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:34,970] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:34,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:34,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651655.1_ASM1465165v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:34,971] [INFO] Task started: Blastn
[2024-01-24 13:33:34,971] [INFO] Running command: blastn -query GCF_014651655.1_ASM1465165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e4ad1e-9aaa-4b28-9e04-894fa12558a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651655.1_ASM1465165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,276] [INFO] Selected 26 target genomes.
[2024-01-24 13:33:36,276] [INFO] Target genome list was writen to GCF_014651655.1_ASM1465165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:36,338] [INFO] Task started: fastANI
[2024-01-24 13:33:36,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg722c484f-d714-4e67-940b-19e305fbe3c7/GCF_014651655.1_ASM1465165v1_genomic.fna.gz --refList GCF_014651655.1_ASM1465165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651655.1_ASM1465165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:54,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:54,050] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:54,051] [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_900106955.1	s__Aidingimonas halophila	99.9979	1274	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Aidingimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008079445.1	s__Aidingimonas lacisalsi	83.1512	824	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Aidingimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202205.1	s__Halomonas sp003202205	78.2233	340	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	78.222	303	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_014651875.1	s__Halomonas_A qijiaojingensis	78.1967	374	1277	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_001971685.1	s__Halomonas_B sp001971685	78.1364	343	1277	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_900100755.1	s__Halomonas_E taeanensis	78.0546	286	1277	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_010977575.1	s__Halomonas_B socia	77.9983	382	1277	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_000265245.1	s__Halomonas smyrnensis	77.9027	273	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_902500215.1	s__Halomonas sp902500215	77.8909	268	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	77.8851	287	1277	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_007989465.1	s__Halomonas halophila	77.8284	285	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_015992245.1	s__Halomonas sp015992245	77.7974	303	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_000409775.1	s__Halomonas_A anticariensis	77.7904	364	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013009075.1	s__Halomonas_B sp013009075	77.7812	270	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	99.96	99.96	1.00	0.99	3	-
GCF_008297955.1	s__Halomonas sp008297955	77.7678	278	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192285.1	s__Halomonas fontilapidosi	77.7611	281	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.17	98.17	0.94	0.94	2	-
GCF_900113605.1	s__Halomonas_C xianhensis	77.7428	272	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009901955.1	s__Halomonas icarae	77.703	254	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.73	97.73	0.87	0.87	2	-
GCF_011742165.1	s__Halomonas bachuensis	77.6597	306	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361885.1	s__Halomonas ventosae_C	77.6088	228	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006540005.1	s__Halomonas halmophila	77.5674	250	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012427705.1	s__Halomonas piezotolerans	77.4569	117	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_013349955.1	s__Halomonas_E taeanensis_B	77.4235	305	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:54,052] [INFO] GTDB search result was written to GCF_014651655.1_ASM1465165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:54,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:54,058] [INFO] DFAST_QC result json was written to GCF_014651655.1_ASM1465165v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:54,059] [INFO] DFAST_QC completed!
[2024-01-24 13:33:54,059] [INFO] Total running time: 0h1m37s