[2024-01-24 11:12:39,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,352] [INFO] DQC Reference Directory: /var/lib/cwl/stga51e17d1-42ef-4949-8eaa-ebdb87000ec2/dqc_reference
[2024-01-24 11:12:40,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,857] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgd092a009-2d59-407b-9744-6745e6224eed/GCF_008329985.2_ASM832998v2_genomic.fna.gz | prodigal -d GCF_008329985.2_ASM832998v2_genomic.fna/cds.fna -a GCF_008329985.2_ASM832998v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:58,484] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:58,485] [INFO] Task started: HMMsearch
[2024-01-24 11:12:58,485] [INFO] Running command: hmmsearch --tblout GCF_008329985.2_ASM832998v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga51e17d1-42ef-4949-8eaa-ebdb87000ec2/dqc_reference/reference_markers.hmm GCF_008329985.2_ASM832998v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:58,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:58,861] [INFO] Found 6/6 markers.
[2024-01-24 11:12:58,906] [INFO] Query marker FASTA was written to GCF_008329985.2_ASM832998v2_genomic.fna/markers.fasta
[2024-01-24 11:12:58,907] [INFO] Task started: Blastn
[2024-01-24 11:12:58,907] [INFO] Running command: blastn -query GCF_008329985.2_ASM832998v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga51e17d1-42ef-4949-8eaa-ebdb87000ec2/dqc_reference/reference_markers.fasta -out GCF_008329985.2_ASM832998v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:59,760] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:59,764] [INFO] Selected 26 target genomes.
[2024-01-24 11:12:59,764] [INFO] Target genome list was writen to GCF_008329985.2_ASM832998v2_genomic.fna/target_genomes.txt
[2024-01-24 11:12:59,788] [INFO] Task started: fastANI
[2024-01-24 11:12:59,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgd092a009-2d59-407b-9744-6745e6224eed/GCF_008329985.2_ASM832998v2_genomic.fna.gz --refList GCF_008329985.2_ASM832998v2_genomic.fna/target_genomes.txt --output GCF_008329985.2_ASM832998v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:19,142] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:19,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga51e17d1-42ef-4949-8eaa-ebdb87000ec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:19,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga51e17d1-42ef-4949-8eaa-ebdb87000ec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:19,160] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:19,160] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:19,160] [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 cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	79.7856	646	1631	95	below_threshold
Halomonas cupida	strain=NBRC 102219	GCA_007991155.1	44933	44933	type	True	79.7383	622	1631	95	below_threshold
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	79.1093	525	1631	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	79.0924	603	1631	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_000470745.1	1178482	1178482	type	True	79.0629	605	1631	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	78.7043	375	1631	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	78.6117	386	1631	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	78.4999	356	1631	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.4863	369	1631	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	78.4777	359	1631	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	78.4218	431	1631	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	78.3532	411	1631	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.3125	361	1631	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.2618	342	1631	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.2595	359	1631	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	78.2	348	1631	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	78.1699	325	1631	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	78.1659	376	1631	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	78.0835	430	1631	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	78.0462	380	1631	95	below_threshold
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	78.0198	335	1631	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.9219	376	1631	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	77.9127	319	1631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:19,162] [INFO] DFAST Taxonomy check result was written to GCF_008329985.2_ASM832998v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:19,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:19,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:19,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga51e17d1-42ef-4949-8eaa-ebdb87000ec2/dqc_reference/checkm_data
[2024-01-24 11:13:19,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:19,217] [INFO] Task started: CheckM
[2024-01-24 11:13:19,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008329985.2_ASM832998v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008329985.2_ASM832998v2_genomic.fna/checkm_input GCF_008329985.2_ASM832998v2_genomic.fna/checkm_result
[2024-01-24 11:14:13,946] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:13,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:13,966] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:13,966] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:13,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008329985.2_ASM832998v2_genomic.fna/markers.fasta)
[2024-01-24 11:14:13,967] [INFO] Task started: Blastn
[2024-01-24 11:14:13,967] [INFO] Running command: blastn -query GCF_008329985.2_ASM832998v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga51e17d1-42ef-4949-8eaa-ebdb87000ec2/dqc_reference/reference_markers_gtdb.fasta -out GCF_008329985.2_ASM832998v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:15,369] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:15,373] [INFO] Selected 21 target genomes.
[2024-01-24 11:14:15,373] [INFO] Target genome list was writen to GCF_008329985.2_ASM832998v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:15,390] [INFO] Task started: fastANI
[2024-01-24 11:14:15,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgd092a009-2d59-407b-9744-6745e6224eed/GCF_008329985.2_ASM832998v2_genomic.fna.gz --refList GCF_008329985.2_ASM832998v2_genomic.fna/target_genomes_gtdb.txt --output GCF_008329985.2_ASM832998v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:31,729] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:31,749] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:31,749] [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_008329985.2	s__Halomonas sp008329985	100.0	1631	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142755.1	s__Halomonas cupida	79.777	647	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003045775.1	s__Halomonas litopenaei	79.0915	527	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	-
GCF_001431725.1	s__Halomonas huangheensis	79.0424	604	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002549795.1	s__Halomonas beimenensis	78.7526	391	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303055.1	s__Halomonas litopenaei_A	78.7445	508	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	78.7108	373	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_000265245.1	s__Halomonas smyrnensis	78.6012	387	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_004798905.1	s__Halomonas borealis	78.4999	356	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017868935.1	s__Halomonas sp017868935	78.4331	355	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	78.431	430	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	78.3725	409	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	78.3119	361	1631	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	78.2196	296	1631	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	78.1965	349	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	78.1738	312	1631	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	78.1464	327	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	78.0579	333	1631	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_000246875.1	s__Halomonas sp000246875	78.0565	347	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192215.1	s__Halomonas cerina	78.0368	381	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011742915.1	s__Halomonas desiderata	78.0208	377	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:31,751] [INFO] GTDB search result was written to GCF_008329985.2_ASM832998v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:31,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:31,756] [INFO] DFAST_QC result json was written to GCF_008329985.2_ASM832998v2_genomic.fna/dqc_result.json
[2024-01-24 11:14:31,756] [INFO] DFAST_QC completed!
[2024-01-24 11:14:31,756] [INFO] Total running time: 0h1m52s