[2023-06-19 04:14:50,808] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:50,813] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:50,813] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb918f1c-c24c-4dbe-b68f-f09a8f7596eb/dqc_reference
[2023-06-19 04:14:52,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:52,641] [INFO] Task started: Prodigal
[2023-06-19 04:14:52,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bc4ab2f-1f88-47ff-a068-d86d742faef9/GCA_018607965.1_ASM1860796v1_genomic.fna.gz | prodigal -d GCA_018607965.1_ASM1860796v1_genomic.fna/cds.fna -a GCA_018607965.1_ASM1860796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:15:01,438] [INFO] Task succeeded: Prodigal
[2023-06-19 04:15:01,438] [INFO] Task started: HMMsearch
[2023-06-19 04:15:01,439] [INFO] Running command: hmmsearch --tblout GCA_018607965.1_ASM1860796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb918f1c-c24c-4dbe-b68f-f09a8f7596eb/dqc_reference/reference_markers.hmm GCA_018607965.1_ASM1860796v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:15:01,698] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:15:01,700] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3bc4ab2f-1f88-47ff-a068-d86d742faef9/GCA_018607965.1_ASM1860796v1_genomic.fna.gz]
[2023-06-19 04:15:01,728] [INFO] Query marker FASTA was written to GCA_018607965.1_ASM1860796v1_genomic.fna/markers.fasta
[2023-06-19 04:15:01,729] [INFO] Task started: Blastn
[2023-06-19 04:15:01,729] [INFO] Running command: blastn -query GCA_018607965.1_ASM1860796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb918f1c-c24c-4dbe-b68f-f09a8f7596eb/dqc_reference/reference_markers.fasta -out GCA_018607965.1_ASM1860796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:02,419] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:02,424] [INFO] Selected 14 target genomes.
[2023-06-19 04:15:02,425] [INFO] Target genome list was writen to GCA_018607965.1_ASM1860796v1_genomic.fna/target_genomes.txt
[2023-06-19 04:15:02,428] [INFO] Task started: fastANI
[2023-06-19 04:15:02,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc4ab2f-1f88-47ff-a068-d86d742faef9/GCA_018607965.1_ASM1860796v1_genomic.fna.gz --refList GCA_018607965.1_ASM1860796v1_genomic.fna/target_genomes.txt --output GCA_018607965.1_ASM1860796v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:15:11,091] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:11,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb918f1c-c24c-4dbe-b68f-f09a8f7596eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:15:11,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb918f1c-c24c-4dbe-b68f-f09a8f7596eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:15:11,105] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:15:11,105] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:15:11,105] [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
Planktotalea frisia	strain=DSM 23709	GCA_003254185.1	696762	696762	type	True	79.1883	478	914	95	below_threshold
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	79.1875	480	914	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	78.6928	406	914	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.377	94	914	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	76.3237	96	914	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.1124	79	914	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.0536	72	914	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	75.9908	74	914	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	75.842	62	914	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	75.7825	99	914	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	75.7707	100	914	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:15:11,107] [INFO] DFAST Taxonomy check result was written to GCA_018607965.1_ASM1860796v1_genomic.fna/tc_result.tsv
[2023-06-19 04:15:11,108] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:15:11,108] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:15:11,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb918f1c-c24c-4dbe-b68f-f09a8f7596eb/dqc_reference/checkm_data
[2023-06-19 04:15:11,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:15:11,141] [INFO] Task started: CheckM
[2023-06-19 04:15:11,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607965.1_ASM1860796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607965.1_ASM1860796v1_genomic.fna/checkm_input GCA_018607965.1_ASM1860796v1_genomic.fna/checkm_result
[2023-06-19 04:15:41,984] [INFO] Task succeeded: CheckM
[2023-06-19 04:15:41,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:15:42,015] [INFO] ===== Completeness check finished =====
[2023-06-19 04:15:42,016] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:15:42,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607965.1_ASM1860796v1_genomic.fna/markers.fasta)
[2023-06-19 04:15:42,016] [INFO] Task started: Blastn
[2023-06-19 04:15:42,017] [INFO] Running command: blastn -query GCA_018607965.1_ASM1860796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb918f1c-c24c-4dbe-b68f-f09a8f7596eb/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607965.1_ASM1860796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:43,212] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:43,216] [INFO] Selected 9 target genomes.
[2023-06-19 04:15:43,216] [INFO] Target genome list was writen to GCA_018607965.1_ASM1860796v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:15:43,220] [INFO] Task started: fastANI
[2023-06-19 04:15:43,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc4ab2f-1f88-47ff-a068-d86d742faef9/GCA_018607965.1_ASM1860796v1_genomic.fna.gz --refList GCA_018607965.1_ASM1860796v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607965.1_ASM1860796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:15:49,200] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:49,212] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:15:49,212] [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_018607965.1	s__Planktotalea sp018607965	100.0	906	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001890925.1	s__Planktotalea frisia	79.1973	479	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	-
GCA_000156115.1	s__Planktotalea sp000156115	78.838	441	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.77	99.74	0.95	0.90	3	-
GCA_018607995.1	s__Planktotalea sp018607995	78.7113	421	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105285.1	s__Planktotalea arctica	78.7023	405	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	76.8447	112	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.2064	104	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	76.196	105	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	75.7111	66	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:15:49,216] [INFO] GTDB search result was written to GCA_018607965.1_ASM1860796v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:15:49,217] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:15:49,221] [INFO] DFAST_QC result json was written to GCA_018607965.1_ASM1860796v1_genomic.fna/dqc_result.json
[2023-06-19 04:15:49,221] [INFO] DFAST_QC completed!
[2023-06-19 04:15:49,221] [INFO] Total running time: 0h0m58s