[2024-01-25 18:12:05,677] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:05,684] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:05,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c83afea-5292-44fe-9dd1-a54d600b57e4/dqc_reference
[2024-01-25 18:12:06,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:06,872] [INFO] Task started: Prodigal
[2024-01-25 18:12:06,873] [INFO] Running command: gunzip -c /var/lib/cwl/stge1f6e1ce-0162-453b-a688-deab41299ec4/GCF_024790395.1_ASM2479039v1_genomic.fna.gz | prodigal -d GCF_024790395.1_ASM2479039v1_genomic.fna/cds.fna -a GCF_024790395.1_ASM2479039v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:16,986] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:16,986] [INFO] Task started: HMMsearch
[2024-01-25 18:12:16,986] [INFO] Running command: hmmsearch --tblout GCF_024790395.1_ASM2479039v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c83afea-5292-44fe-9dd1-a54d600b57e4/dqc_reference/reference_markers.hmm GCF_024790395.1_ASM2479039v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:17,212] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:17,213] [INFO] Found 6/6 markers.
[2024-01-25 18:12:17,245] [INFO] Query marker FASTA was written to GCF_024790395.1_ASM2479039v1_genomic.fna/markers.fasta
[2024-01-25 18:12:17,245] [INFO] Task started: Blastn
[2024-01-25 18:12:17,245] [INFO] Running command: blastn -query GCF_024790395.1_ASM2479039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c83afea-5292-44fe-9dd1-a54d600b57e4/dqc_reference/reference_markers.fasta -out GCF_024790395.1_ASM2479039v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:18,038] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:18,042] [INFO] Selected 27 target genomes.
[2024-01-25 18:12:18,042] [INFO] Target genome list was writen to GCF_024790395.1_ASM2479039v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:18,053] [INFO] Task started: fastANI
[2024-01-25 18:12:18,053] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f6e1ce-0162-453b-a688-deab41299ec4/GCF_024790395.1_ASM2479039v1_genomic.fna.gz --refList GCF_024790395.1_ASM2479039v1_genomic.fna/target_genomes.txt --output GCF_024790395.1_ASM2479039v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:36,757] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:36,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c83afea-5292-44fe-9dd1-a54d600b57e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:36,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c83afea-5292-44fe-9dd1-a54d600b57e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:36,772] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:12:36,772] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:12:36,772] [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
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	79.6898	577	1305	95	below_threshold
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	79.6298	500	1305	95	below_threshold
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	79.4853	507	1305	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	79.3176	456	1305	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	79.2803	421	1305	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.2625	396	1305	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	79.2131	409	1305	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.1394	444	1305	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	79.1282	397	1305	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	79.0968	456	1305	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	79.0924	437	1305	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	79.0423	393	1305	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	79.0331	437	1305	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.0151	451	1305	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.9393	456	1305	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	78.848	407	1305	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.8411	429	1305	95	below_threshold
Halomonas fontilapidosi	strain=CECT 7341	GCA_014192285.1	616675	616675	type	True	78.758	357	1305	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	78.7292	410	1305	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	78.7283	349	1305	95	below_threshold
Halomonas subglaciescola	strain=ACAM 12	GCA_900142895.1	29571	29571	type	True	78.6433	360	1305	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	78.6174	408	1305	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.6024	406	1305	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	78.321	340	1305	95	below_threshold
Halomonas lutea	strain=DSM 23508	GCA_000378505.1	453962	453962	type	True	77.7972	240	1305	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	76.7045	69	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:36,773] [INFO] DFAST Taxonomy check result was written to GCF_024790395.1_ASM2479039v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:36,776] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:36,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:36,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c83afea-5292-44fe-9dd1-a54d600b57e4/dqc_reference/checkm_data
[2024-01-25 18:12:36,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:36,817] [INFO] Task started: CheckM
[2024-01-25 18:12:36,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024790395.1_ASM2479039v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024790395.1_ASM2479039v1_genomic.fna/checkm_input GCF_024790395.1_ASM2479039v1_genomic.fna/checkm_result
[2024-01-25 18:13:08,579] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:08,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:08,598] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:08,599] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:08,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024790395.1_ASM2479039v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:08,599] [INFO] Task started: Blastn
[2024-01-25 18:13:08,599] [INFO] Running command: blastn -query GCF_024790395.1_ASM2479039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c83afea-5292-44fe-9dd1-a54d600b57e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_024790395.1_ASM2479039v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:09,940] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:09,943] [INFO] Selected 27 target genomes.
[2024-01-25 18:13:09,943] [INFO] Target genome list was writen to GCF_024790395.1_ASM2479039v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:09,963] [INFO] Task started: fastANI
[2024-01-25 18:13:09,963] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f6e1ce-0162-453b-a688-deab41299ec4/GCF_024790395.1_ASM2479039v1_genomic.fna.gz --refList GCF_024790395.1_ASM2479039v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024790395.1_ASM2479039v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:29,463] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:29,478] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:13:29,479] [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_003002925.1	s__Halomonas songnenensis	79.6898	577	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	79.6302	500	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_000275725.1	s__Halomonas stevensii	79.4856	507	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_003056305.1	s__Halomonas denitrificans	79.3335	455	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	79.2685	395	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_009846525.1	s__Halomonas sp002696125	79.2673	417	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCA_011742915.1	s__Halomonas desiderata	79.2539	439	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
GCF_007989465.1	s__Halomonas halophila	79.2463	424	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_900116405.1	s__Halomonas saccharevitans	79.2007	411	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015992245.1	s__Halomonas sp015992245	79.1094	452	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_003254665.1	s__Halomonas lactosivorans	79.106	456	1305	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	79.1053	399	1305	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	79.1029	436	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_003202205.1	s__Halomonas sp003202205	79.048	427	1305	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	78.9887	413	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCA_018401555.1	s__Halomonas sp018401555	78.9488	363	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742165.1	s__Halomonas bachuensis	78.8307	408	1305	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	78.7581	357	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.17	98.17	0.94	0.94	2	-
GCF_900142895.1	s__Halomonas subglaciescola	78.6433	360	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013697085.1	s__Halomonas kenyensis	78.607	409	1305	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	78.5833	339	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900961225.1	s__Halomonas_C sp900961225	78.544	365	1305	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_003206135.1	s__Salinicola salarius	78.4499	310	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCF_004117855.1	s__Halomonas_C coralii	78.4219	376	1305	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_014652715.1	s__Salinicola rhizosphaerae	78.2084	286	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179555.1	s__Salinicola salarius_A	78.1765	299	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298015.1	s__Salinicola sp008298015	77.873	262	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:29,480] [INFO] GTDB search result was written to GCF_024790395.1_ASM2479039v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:29,481] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:29,485] [INFO] DFAST_QC result json was written to GCF_024790395.1_ASM2479039v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:29,485] [INFO] DFAST_QC completed!
[2024-01-25 18:13:29,485] [INFO] Total running time: 0h1m24s