[2023-06-19 15:21:21,623] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:21:21,627] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:21:21,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg70d4df0a-ff96-44a2-966d-42bc8c926d49/dqc_reference
[2023-06-19 15:21:24,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:21:24,506] [INFO] Task started: Prodigal
[2023-06-19 15:21:24,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b5e38ab-90cd-4f76-9c09-1ee9493a5995/GCA_013360685.1_ASM1336068v1_genomic.fna.gz | prodigal -d GCA_013360685.1_ASM1336068v1_genomic.fna/cds.fna -a GCA_013360685.1_ASM1336068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:21:48,893] [INFO] Task succeeded: Prodigal
[2023-06-19 15:21:48,894] [INFO] Task started: HMMsearch
[2023-06-19 15:21:48,894] [INFO] Running command: hmmsearch --tblout GCA_013360685.1_ASM1336068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70d4df0a-ff96-44a2-966d-42bc8c926d49/dqc_reference/reference_markers.hmm GCA_013360685.1_ASM1336068v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:21:49,247] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:21:49,250] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0b5e38ab-90cd-4f76-9c09-1ee9493a5995/GCA_013360685.1_ASM1336068v1_genomic.fna.gz]
[2023-06-19 15:21:49,313] [INFO] Query marker FASTA was written to GCA_013360685.1_ASM1336068v1_genomic.fna/markers.fasta
[2023-06-19 15:21:49,314] [INFO] Task started: Blastn
[2023-06-19 15:21:49,314] [INFO] Running command: blastn -query GCA_013360685.1_ASM1336068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70d4df0a-ff96-44a2-966d-42bc8c926d49/dqc_reference/reference_markers.fasta -out GCA_013360685.1_ASM1336068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:21:49,974] [INFO] Task succeeded: Blastn
[2023-06-19 15:21:49,981] [INFO] Selected 15 target genomes.
[2023-06-19 15:21:49,982] [INFO] Target genome list was writen to GCA_013360685.1_ASM1336068v1_genomic.fna/target_genomes.txt
[2023-06-19 15:21:49,987] [INFO] Task started: fastANI
[2023-06-19 15:21:49,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b5e38ab-90cd-4f76-9c09-1ee9493a5995/GCA_013360685.1_ASM1336068v1_genomic.fna.gz --refList GCA_013360685.1_ASM1336068v1_genomic.fna/target_genomes.txt --output GCA_013360685.1_ASM1336068v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 15:22:03,574] [INFO] Task succeeded: fastANI
[2023-06-19 15:22:03,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70d4df0a-ff96-44a2-966d-42bc8c926d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 15:22:03,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70d4df0a-ff96-44a2-966d-42bc8c926d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 15:22:03,599] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 15:22:03,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 15:22:03,600] [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
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.5474	126	2379	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.5091	102	2379	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.4082	126	2379	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.2866	79	2379	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.1761	79	2379	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.159	123	2379	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.0383	161	2379	95	below_threshold
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	74.7115	50	2379	95	below_threshold
Stutzerimonas balearica	strain=DSM 6083	GCA_900103375.1	74829	74829	type	True	74.7115	50	2379	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	74.6524	61	2379	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 15:22:03,602] [INFO] DFAST Taxonomy check result was written to GCA_013360685.1_ASM1336068v1_genomic.fna/tc_result.tsv
[2023-06-19 15:22:03,602] [INFO] ===== Taxonomy check completed =====
[2023-06-19 15:22:03,603] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:22:03,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70d4df0a-ff96-44a2-966d-42bc8c926d49/dqc_reference/checkm_data
[2023-06-19 15:22:03,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:22:03,679] [INFO] Task started: CheckM
[2023-06-19 15:22:03,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013360685.1_ASM1336068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013360685.1_ASM1336068v1_genomic.fna/checkm_input GCA_013360685.1_ASM1336068v1_genomic.fna/checkm_result
[2023-06-19 15:23:11,252] [INFO] Task succeeded: CheckM
[2023-06-19 15:23:11,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 15:23:11,282] [INFO] ===== Completeness check finished =====
[2023-06-19 15:23:11,282] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:23:11,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013360685.1_ASM1336068v1_genomic.fna/markers.fasta)
[2023-06-19 15:23:11,283] [INFO] Task started: Blastn
[2023-06-19 15:23:11,283] [INFO] Running command: blastn -query GCA_013360685.1_ASM1336068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70d4df0a-ff96-44a2-966d-42bc8c926d49/dqc_reference/reference_markers_gtdb.fasta -out GCA_013360685.1_ASM1336068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:23:12,274] [INFO] Task succeeded: Blastn
[2023-06-19 15:23:12,280] [INFO] Selected 12 target genomes.
[2023-06-19 15:23:12,280] [INFO] Target genome list was writen to GCA_013360685.1_ASM1336068v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:23:12,288] [INFO] Task started: fastANI
[2023-06-19 15:23:12,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b5e38ab-90cd-4f76-9c09-1ee9493a5995/GCA_013360685.1_ASM1336068v1_genomic.fna.gz --refList GCA_013360685.1_ASM1336068v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013360685.1_ASM1336068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:23:25,422] [INFO] Task succeeded: fastANI
[2023-06-19 15:23:25,434] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:23:25,434] [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_013360685.1	s__JABWBD01 sp013360685	100.0	2349	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012728855.1	s__JABWBD01 sp012728855	78.5851	883	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744395.1	s__JAAYCB01 sp012744395	76.8196	256	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAAYCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367845.1	s__DSXL01 sp011367845	76.2697	259	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__DSXL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119795.1	s__SKOZ01 sp007119795	76.1467	118	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__SKOZ01	95.0	99.25	99.25	0.71	0.71	2	-
GCA_018897395.1	s__JAHIKV01 sp018897395	76.1415	136	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAHIKV01	95.0	99.63	99.63	0.95	0.95	2	-
GCA_016928165.1	s__JAHIKV01 sp016928165	76.0478	124	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAHIKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931995.1	s__JAFGDS01 sp016931995	75.9819	196	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	75.3242	114	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308215.1	s__Urbifossiella sp017308215	74.7574	132	2379	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 15:23:25,437] [INFO] GTDB search result was written to GCA_013360685.1_ASM1336068v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:23:25,437] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:23:25,441] [INFO] DFAST_QC result json was written to GCA_013360685.1_ASM1336068v1_genomic.fna/dqc_result.json
[2023-06-19 15:23:25,441] [INFO] DFAST_QC completed!
[2023-06-19 15:23:25,441] [INFO] Total running time: 0h2m4s