[2023-06-17 02:35:34,494] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:35:34,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:35:34,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c419a9a-54c5-4611-bde0-5336f149f6a1/dqc_reference
[2023-06-17 02:35:36,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:35:36,191] [INFO] Task started: Prodigal
[2023-06-17 02:35:36,192] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf7c1c34-f421-4bad-b627-573ced4c5962/GCA_013041925.1_ASM1304192v1_genomic.fna.gz | prodigal -d GCA_013041925.1_ASM1304192v1_genomic.fna/cds.fna -a GCA_013041925.1_ASM1304192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:35:56,626] [INFO] Task succeeded: Prodigal
[2023-06-17 02:35:56,627] [INFO] Task started: HMMsearch
[2023-06-17 02:35:56,627] [INFO] Running command: hmmsearch --tblout GCA_013041925.1_ASM1304192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c419a9a-54c5-4611-bde0-5336f149f6a1/dqc_reference/reference_markers.hmm GCA_013041925.1_ASM1304192v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:35:56,920] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:35:56,922] [INFO] Found 6/6 markers.
[2023-06-17 02:35:56,968] [INFO] Query marker FASTA was written to GCA_013041925.1_ASM1304192v1_genomic.fna/markers.fasta
[2023-06-17 02:35:56,968] [INFO] Task started: Blastn
[2023-06-17 02:35:56,968] [INFO] Running command: blastn -query GCA_013041925.1_ASM1304192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c419a9a-54c5-4611-bde0-5336f149f6a1/dqc_reference/reference_markers.fasta -out GCA_013041925.1_ASM1304192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:35:57,584] [INFO] Task succeeded: Blastn
[2023-06-17 02:35:57,590] [INFO] Selected 20 target genomes.
[2023-06-17 02:35:57,591] [INFO] Target genome list was writen to GCA_013041925.1_ASM1304192v1_genomic.fna/target_genomes.txt
[2023-06-17 02:35:57,597] [INFO] Task started: fastANI
[2023-06-17 02:35:57,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf7c1c34-f421-4bad-b627-573ced4c5962/GCA_013041925.1_ASM1304192v1_genomic.fna.gz --refList GCA_013041925.1_ASM1304192v1_genomic.fna/target_genomes.txt --output GCA_013041925.1_ASM1304192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:36:11,988] [INFO] Task succeeded: fastANI
[2023-06-17 02:36:11,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c419a9a-54c5-4611-bde0-5336f149f6a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:36:11,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c419a9a-54c5-4611-bde0-5336f149f6a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:36:11,994] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:36:11,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 02:36:11,994] [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
Oceaniferula marina	strain=N1E253	GCA_013391475.1	2748318	2748318	type	True	76.844	155	1076	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 02:36:11,997] [INFO] DFAST Taxonomy check result was written to GCA_013041925.1_ASM1304192v1_genomic.fna/tc_result.tsv
[2023-06-17 02:36:11,997] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:36:11,998] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:36:11,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c419a9a-54c5-4611-bde0-5336f149f6a1/dqc_reference/checkm_data
[2023-06-17 02:36:12,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:36:12,046] [INFO] Task started: CheckM
[2023-06-17 02:36:12,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013041925.1_ASM1304192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013041925.1_ASM1304192v1_genomic.fna/checkm_input GCA_013041925.1_ASM1304192v1_genomic.fna/checkm_result
[2023-06-17 02:37:11,747] [INFO] Task succeeded: CheckM
[2023-06-17 02:37:11,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:37:11,770] [INFO] ===== Completeness check finished =====
[2023-06-17 02:37:11,770] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:37:11,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013041925.1_ASM1304192v1_genomic.fna/markers.fasta)
[2023-06-17 02:37:11,771] [INFO] Task started: Blastn
[2023-06-17 02:37:11,771] [INFO] Running command: blastn -query GCA_013041925.1_ASM1304192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c419a9a-54c5-4611-bde0-5336f149f6a1/dqc_reference/reference_markers_gtdb.fasta -out GCA_013041925.1_ASM1304192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:37:12,563] [INFO] Task succeeded: Blastn
[2023-06-17 02:37:12,582] [INFO] Selected 18 target genomes.
[2023-06-17 02:37:12,582] [INFO] Target genome list was writen to GCA_013041925.1_ASM1304192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:37:12,597] [INFO] Task started: fastANI
[2023-06-17 02:37:12,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf7c1c34-f421-4bad-b627-573ced4c5962/GCA_013041925.1_ASM1304192v1_genomic.fna.gz --refList GCA_013041925.1_ASM1304192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013041925.1_ASM1304192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:37:23,148] [INFO] Task succeeded: fastANI
[2023-06-17 02:37:23,158] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:37:23,158] [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_013041925.1	s__UBA985 sp013041925	100.0	1074	1076	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_016811075.1	s__UBA985 sp016811075	77.4756	202	1076	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCA_009937455.1	s__UBA985 sp009937455	77.2447	85	1076	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292185.1	s__UBA985 sp002292185	77.2366	82	1076	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	98.24	97.16	0.73	0.70	3	-
GCA_017857425.1	s__UBA985 sp017857425	76.9759	93	1076	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	96.59	96.59	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-17 02:37:23,160] [INFO] GTDB search result was written to GCA_013041925.1_ASM1304192v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:37:23,161] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:37:23,164] [INFO] DFAST_QC result json was written to GCA_013041925.1_ASM1304192v1_genomic.fna/dqc_result.json
[2023-06-17 02:37:23,164] [INFO] DFAST_QC completed!
[2023-06-17 02:37:23,164] [INFO] Total running time: 0h1m49s