[2024-01-24 14:06:14,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,430] [INFO] DQC Reference Directory: /var/lib/cwl/stgae1d8821-c874-476c-84f6-1bfe32852726/dqc_reference
[2024-01-24 14:06:15,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:15,867] [INFO] Task started: Prodigal
[2024-01-24 14:06:15,867] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0aae241-004f-4310-880b-fe52994e174a/GCF_014652375.1_ASM1465237v1_genomic.fna.gz | prodigal -d GCF_014652375.1_ASM1465237v1_genomic.fna/cds.fna -a GCF_014652375.1_ASM1465237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:24,418] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:24,419] [INFO] Task started: HMMsearch
[2024-01-24 14:06:24,419] [INFO] Running command: hmmsearch --tblout GCF_014652375.1_ASM1465237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae1d8821-c874-476c-84f6-1bfe32852726/dqc_reference/reference_markers.hmm GCF_014652375.1_ASM1465237v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:24,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:24,716] [INFO] Found 6/6 markers.
[2024-01-24 14:06:24,751] [INFO] Query marker FASTA was written to GCF_014652375.1_ASM1465237v1_genomic.fna/markers.fasta
[2024-01-24 14:06:24,751] [INFO] Task started: Blastn
[2024-01-24 14:06:24,751] [INFO] Running command: blastn -query GCF_014652375.1_ASM1465237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae1d8821-c874-476c-84f6-1bfe32852726/dqc_reference/reference_markers.fasta -out GCF_014652375.1_ASM1465237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:25,521] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:25,526] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:25,527] [INFO] Target genome list was writen to GCF_014652375.1_ASM1465237v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:25,545] [INFO] Task started: fastANI
[2024-01-24 14:06:25,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0aae241-004f-4310-880b-fe52994e174a/GCF_014652375.1_ASM1465237v1_genomic.fna.gz --refList GCF_014652375.1_ASM1465237v1_genomic.fna/target_genomes.txt --output GCF_014652375.1_ASM1465237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:40,910] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:40,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae1d8821-c874-476c-84f6-1bfe32852726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:40,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae1d8821-c874-476c-84f6-1bfe32852726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:40,928] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:40,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:40,929] [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
Alishewanella tabrizica	strain=KCTC 23723	GCA_014652375.1	671278	671278	type	True	100.0	1226	1227	95	conclusive
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	81.4658	606	1227	95	below_threshold
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	79.6299	353	1227	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	79.3702	349	1227	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	79.1964	355	1227	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.7606	220	1227	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	78.4956	224	1227	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	78.285	221	1227	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	78.2026	248	1227	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.1805	223	1227	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	77.7515	148	1227	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	75.8692	50	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:40,930] [INFO] DFAST Taxonomy check result was written to GCF_014652375.1_ASM1465237v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:40,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:40,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:40,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae1d8821-c874-476c-84f6-1bfe32852726/dqc_reference/checkm_data
[2024-01-24 14:06:40,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:40,974] [INFO] Task started: CheckM
[2024-01-24 14:06:40,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652375.1_ASM1465237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652375.1_ASM1465237v1_genomic.fna/checkm_input GCF_014652375.1_ASM1465237v1_genomic.fna/checkm_result
[2024-01-24 14:07:11,626] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:11,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:11,649] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:11,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:11,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652375.1_ASM1465237v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:11,650] [INFO] Task started: Blastn
[2024-01-24 14:07:11,651] [INFO] Running command: blastn -query GCF_014652375.1_ASM1465237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae1d8821-c874-476c-84f6-1bfe32852726/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652375.1_ASM1465237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:12,830] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:12,835] [INFO] Selected 18 target genomes.
[2024-01-24 14:07:12,835] [INFO] Target genome list was writen to GCF_014652375.1_ASM1465237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:12,859] [INFO] Task started: fastANI
[2024-01-24 14:07:12,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0aae241-004f-4310-880b-fe52994e174a/GCF_014652375.1_ASM1465237v1_genomic.fna.gz --refList GCF_014652375.1_ASM1465237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652375.1_ASM1465237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:25,098] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:25,116] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:25,116] [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_014652375.1	s__Alishewanella tabrizica	100.0	1226	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014653435.1	s__Alishewanella longhuensis	81.4775	605	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000280055.1	s__Alishewanella aestuarii	79.6222	354	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	96.26	96.26	0.87	0.87	2	-
GCF_000245735.1	s__Alishewanella jeotgali	79.3824	348	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	N/A	N/A	N/A	N/A	1	-
GCF_000272005.1	s__Alishewanella agri	79.1964	355	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	96.64	95.87	0.84	0.80	3	-
GCF_004345025.1	s__Rheinheimera sp004345025	78.6428	189	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	78.51	246	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	78.4956	224	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	78.4176	231	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	78.2898	220	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634895.1	s__Rheinheimera pleomorphica	78.2036	221	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382165.1	s__Arsukibacterium perlucidum	78.2026	248	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415085.1	s__Arsukibacterium sp002415085	78.0151	206	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	-
GCF_003990335.1	s__Pararheinheimera sp003990335	77.8344	135	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364615.1	s__Arsukibacterium sp002364615	77.8116	228	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_004005945.1	s__Pararheinheimera riviphila	77.7515	148	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001669775.1	s__Pararheinheimera sp001669775	77.6052	153	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:25,118] [INFO] GTDB search result was written to GCF_014652375.1_ASM1465237v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:25,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:25,123] [INFO] DFAST_QC result json was written to GCF_014652375.1_ASM1465237v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:25,123] [INFO] DFAST_QC completed!
[2024-01-24 14:07:25,123] [INFO] Total running time: 0h1m11s