[2024-01-24 12:45:09,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f36c64a-6aa9-4b46-b2f4-97185fc1329d/dqc_reference
[2024-01-24 12:45:13,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,084] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,084] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0886740-179e-4265-8311-350d8c39aeb4/GCF_007989625.1_ASM798962v1_genomic.fna.gz | prodigal -d GCF_007989625.1_ASM798962v1_genomic.fna/cds.fna -a GCF_007989625.1_ASM798962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:23,583] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:23,584] [INFO] Task started: HMMsearch
[2024-01-24 12:45:23,584] [INFO] Running command: hmmsearch --tblout GCF_007989625.1_ASM798962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f36c64a-6aa9-4b46-b2f4-97185fc1329d/dqc_reference/reference_markers.hmm GCF_007989625.1_ASM798962v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:23,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:23,869] [INFO] Found 6/6 markers.
[2024-01-24 12:45:23,906] [INFO] Query marker FASTA was written to GCF_007989625.1_ASM798962v1_genomic.fna/markers.fasta
[2024-01-24 12:45:23,906] [INFO] Task started: Blastn
[2024-01-24 12:45:23,906] [INFO] Running command: blastn -query GCF_007989625.1_ASM798962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f36c64a-6aa9-4b46-b2f4-97185fc1329d/dqc_reference/reference_markers.fasta -out GCF_007989625.1_ASM798962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:24,899] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:24,906] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:24,907] [INFO] Target genome list was writen to GCF_007989625.1_ASM798962v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:24,916] [INFO] Task started: fastANI
[2024-01-24 12:45:24,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0886740-179e-4265-8311-350d8c39aeb4/GCF_007989625.1_ASM798962v1_genomic.fna.gz --refList GCF_007989625.1_ASM798962v1_genomic.fna/target_genomes.txt --output GCF_007989625.1_ASM798962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:40,098] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:40,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f36c64a-6aa9-4b46-b2f4-97185fc1329d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:40,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f36c64a-6aa9-4b46-b2f4-97185fc1329d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:40,117] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:40,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:40,118] [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 pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	100.0	1223	1229	95	conclusive
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	83.8723	748	1229	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	83.6453	728	1229	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	83.606	833	1229	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	83.5915	802	1229	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.3126	763	1229	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	83.2919	749	1229	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	83.2858	778	1229	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	83.2183	770	1229	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	82.9049	782	1229	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	82.8393	672	1229	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	82.7461	694	1229	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	82.6574	715	1229	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.2528	718	1229	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.3849	717	1229	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	81.22	701	1229	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	81.2175	683	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:40,120] [INFO] DFAST Taxonomy check result was written to GCF_007989625.1_ASM798962v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:40,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:40,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:40,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f36c64a-6aa9-4b46-b2f4-97185fc1329d/dqc_reference/checkm_data
[2024-01-24 12:45:40,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:40,168] [INFO] Task started: CheckM
[2024-01-24 12:45:40,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989625.1_ASM798962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989625.1_ASM798962v1_genomic.fna/checkm_input GCF_007989625.1_ASM798962v1_genomic.fna/checkm_result
[2024-01-24 12:46:13,595] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:13,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:13,616] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:13,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:13,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989625.1_ASM798962v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:13,617] [INFO] Task started: Blastn
[2024-01-24 12:46:13,618] [INFO] Running command: blastn -query GCF_007989625.1_ASM798962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f36c64a-6aa9-4b46-b2f4-97185fc1329d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989625.1_ASM798962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:15,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:15,196] [INFO] Selected 18 target genomes.
[2024-01-24 12:46:15,197] [INFO] Target genome list was writen to GCF_007989625.1_ASM798962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:15,229] [INFO] Task started: fastANI
[2024-01-24 12:46:15,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0886740-179e-4265-8311-350d8c39aeb4/GCF_007989625.1_ASM798962v1_genomic.fna.gz --refList GCF_007989625.1_ASM798962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989625.1_ASM798962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:29,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:29,796] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:29,796] [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_007989625.1	s__Halomonas_F pacifica	100.0	1223	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	98.81	98.81	0.96	0.96	2	conclusive
GCF_015645095.1	s__Halomonas_F sp015645095	91.377	989	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	83.841	751	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	83.7206	679	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_900104135.1	s__Halomonas shengliensis	83.6382	728	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_002879645.1	s__Halomonas heilongjiangensis	83.5786	804	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009363755.1	s__Halomonas sp009363755	83.4607	733	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	83.2168	771	1229	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	83.1893	615	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	83.0647	525	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	83.0377	802	1229	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	82.9609	601	1229	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	82.9159	781	1229	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	82.8111	688	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCA_004551485.1	s__Halomonas azerbaijanica	82.5502	759	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846525.1	s__Halomonas sp002696125	78.1136	292	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCA_003242275.1	s__ZC4RG30 sp003242275	76.3319	146	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272825.1	s__GCA-2722315 sp012272825	76.0063	126	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:29,798] [INFO] GTDB search result was written to GCF_007989625.1_ASM798962v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:29,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:29,806] [INFO] DFAST_QC result json was written to GCF_007989625.1_ASM798962v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:29,807] [INFO] DFAST_QC completed!
[2024-01-24 12:46:29,807] [INFO] Total running time: 0h1m20s