[2023-06-30 09:59:39,512] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:59:39,525] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:59:39,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfec0280-396e-4884-a514-e0d9b7eb4e44/dqc_reference
[2023-06-30 09:59:40,834] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:59:40,835] [INFO] Task started: Prodigal
[2023-06-30 09:59:40,835] [INFO] Running command: gunzip -c /var/lib/cwl/stga7f9ec4d-f241-4c34-adc8-6efa70ca9000/GCA_016708925.1_ASM1670892v1_genomic.fna.gz | prodigal -d GCA_016708925.1_ASM1670892v1_genomic.fna/cds.fna -a GCA_016708925.1_ASM1670892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:59:50,376] [INFO] Task succeeded: Prodigal
[2023-06-30 09:59:50,376] [INFO] Task started: HMMsearch
[2023-06-30 09:59:50,376] [INFO] Running command: hmmsearch --tblout GCA_016708925.1_ASM1670892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfec0280-396e-4884-a514-e0d9b7eb4e44/dqc_reference/reference_markers.hmm GCA_016708925.1_ASM1670892v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:59:50,634] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:59:50,636] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga7f9ec4d-f241-4c34-adc8-6efa70ca9000/GCA_016708925.1_ASM1670892v1_genomic.fna.gz]
[2023-06-30 09:59:50,663] [INFO] Query marker FASTA was written to GCA_016708925.1_ASM1670892v1_genomic.fna/markers.fasta
[2023-06-30 09:59:50,664] [INFO] Task started: Blastn
[2023-06-30 09:59:50,664] [INFO] Running command: blastn -query GCA_016708925.1_ASM1670892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfec0280-396e-4884-a514-e0d9b7eb4e44/dqc_reference/reference_markers.fasta -out GCA_016708925.1_ASM1670892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:59:51,411] [INFO] Task succeeded: Blastn
[2023-06-30 09:59:51,416] [INFO] Selected 25 target genomes.
[2023-06-30 09:59:51,416] [INFO] Target genome list was writen to GCA_016708925.1_ASM1670892v1_genomic.fna/target_genomes.txt
[2023-06-30 09:59:51,417] [INFO] Task started: fastANI
[2023-06-30 09:59:51,417] [INFO] Running command: fastANI --query /var/lib/cwl/stga7f9ec4d-f241-4c34-adc8-6efa70ca9000/GCA_016708925.1_ASM1670892v1_genomic.fna.gz --refList GCA_016708925.1_ASM1670892v1_genomic.fna/target_genomes.txt --output GCA_016708925.1_ASM1670892v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:00:10,717] [INFO] Task succeeded: fastANI
[2023-06-30 10:00:10,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfec0280-396e-4884-a514-e0d9b7eb4e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:00:10,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfec0280-396e-4884-a514-e0d9b7eb4e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:00:10,734] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:00:10,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:00:10,735] [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
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	77.0018	114	1012	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	76.9732	63	1012	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.9538	86	1012	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	76.871	139	1012	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	76.8684	139	1012	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.8128	132	1012	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.7992	112	1012	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.754	105	1012	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	76.5909	57	1012	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	76.5064	94	1012	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4797	154	1012	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	76.4132	114	1012	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.3904	138	1012	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	76.3867	65	1012	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	76.373	112	1012	95	below_threshold
Thiopseudomonas denitrificans	strain=DSM 28679	GCA_004363035.1	1501432	1501432	type	True	76.3603	50	1012	95	below_threshold
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	76.3498	74	1012	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.2433	135	1012	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	76.0615	60	1012	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.0235	84	1012	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	76.0198	73	1012	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	75.7327	67	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:00:10,737] [INFO] DFAST Taxonomy check result was written to GCA_016708925.1_ASM1670892v1_genomic.fna/tc_result.tsv
[2023-06-30 10:00:10,737] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:00:10,737] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:00:10,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfec0280-396e-4884-a514-e0d9b7eb4e44/dqc_reference/checkm_data
[2023-06-30 10:00:10,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:00:10,775] [INFO] Task started: CheckM
[2023-06-30 10:00:10,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708925.1_ASM1670892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708925.1_ASM1670892v1_genomic.fna/checkm_input GCA_016708925.1_ASM1670892v1_genomic.fna/checkm_result
[2023-06-30 10:00:42,574] [INFO] Task succeeded: CheckM
[2023-06-30 10:00:42,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:00:42,599] [INFO] ===== Completeness check finished =====
[2023-06-30 10:00:42,600] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:00:42,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708925.1_ASM1670892v1_genomic.fna/markers.fasta)
[2023-06-30 10:00:42,601] [INFO] Task started: Blastn
[2023-06-30 10:00:42,601] [INFO] Running command: blastn -query GCA_016708925.1_ASM1670892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfec0280-396e-4884-a514-e0d9b7eb4e44/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708925.1_ASM1670892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:00:43,596] [INFO] Task succeeded: Blastn
[2023-06-30 10:00:43,601] [INFO] Selected 16 target genomes.
[2023-06-30 10:00:43,601] [INFO] Target genome list was writen to GCA_016708925.1_ASM1670892v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:00:43,607] [INFO] Task started: fastANI
[2023-06-30 10:00:43,607] [INFO] Running command: fastANI --query /var/lib/cwl/stga7f9ec4d-f241-4c34-adc8-6efa70ca9000/GCA_016708925.1_ASM1670892v1_genomic.fna.gz --refList GCA_016708925.1_ASM1670892v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708925.1_ASM1670892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:00:55,141] [INFO] Task succeeded: fastANI
[2023-06-30 10:00:55,156] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:00:55,156] [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
GCA_016708925.1	s__JAGPUQ01 sp016708925	100.0	1011	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01	95.0	98.16	98.04	0.89	0.89	3	conclusive
GCA_016191205.1	s__JAGPUQ01 sp016191205	91.8484	632	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018069465.1	s__50-400-T64 sp018069465	76.7042	77	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002943415.1	s__Perlucidibaca sp002943415	76.5585	91	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.4764	140	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356535.2	s__Pseudomonas_E sp002356535	76.4213	68	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.89	96.62	0.90	0.88	3	-
GCF_001651805.1	s__Marinobacterium_A aestuarii	76.3868	65	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577635.1	s__Halomonas_C sp001577635	76.3814	128	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262975.1	s__JADFDG01 sp018262975	76.3687	111	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__JADFDG01;g__JADFDG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720485.1	s__Cobetia marina	76.3253	75	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	-
GCF_008807415.1	s__Pseudomonas sp002079985	76.3075	134	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	97.48	95.53	0.92	0.91	9	-
GCF_000327045.1	s__Thioflavicoccus mobilis	76.0669	66	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	76.0235	84	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_016583835.1	s__Thiococcus pfennigii	75.6446	74	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCF_001297015.1	s__Pseudomonas_E sp001297015	75.6425	71	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.77	0.95	0.94	9	-
GCA_018242485.1	s__SZAS-103 sp018242485	75.502	67	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:00:55,159] [INFO] GTDB search result was written to GCA_016708925.1_ASM1670892v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:00:55,159] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:00:55,163] [INFO] DFAST_QC result json was written to GCA_016708925.1_ASM1670892v1_genomic.fna/dqc_result.json
[2023-06-30 10:00:55,164] [INFO] DFAST_QC completed!
[2023-06-30 10:00:55,164] [INFO] Total running time: 0h1m16s