[2024-01-25 19:46:50,696] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:50,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:50,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg5058f238-b6ec-4d55-86e6-4a45a4006b2f/dqc_reference
[2024-01-25 19:46:51,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:51,913] [INFO] Task started: Prodigal
[2024-01-25 19:46:51,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg485c31c2-616e-4adb-b1ad-facf8817148b/GCF_014773395.1_ASM1477339v1_genomic.fna.gz | prodigal -d GCF_014773395.1_ASM1477339v1_genomic.fna/cds.fna -a GCF_014773395.1_ASM1477339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:02,974] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:02,975] [INFO] Task started: HMMsearch
[2024-01-25 19:47:02,975] [INFO] Running command: hmmsearch --tblout GCF_014773395.1_ASM1477339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5058f238-b6ec-4d55-86e6-4a45a4006b2f/dqc_reference/reference_markers.hmm GCF_014773395.1_ASM1477339v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:03,283] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:03,284] [INFO] Found 6/6 markers.
[2024-01-25 19:47:03,320] [INFO] Query marker FASTA was written to GCF_014773395.1_ASM1477339v1_genomic.fna/markers.fasta
[2024-01-25 19:47:03,321] [INFO] Task started: Blastn
[2024-01-25 19:47:03,321] [INFO] Running command: blastn -query GCF_014773395.1_ASM1477339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5058f238-b6ec-4d55-86e6-4a45a4006b2f/dqc_reference/reference_markers.fasta -out GCF_014773395.1_ASM1477339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:04,054] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:04,057] [INFO] Selected 23 target genomes.
[2024-01-25 19:47:04,057] [INFO] Target genome list was writen to GCF_014773395.1_ASM1477339v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:04,070] [INFO] Task started: fastANI
[2024-01-25 19:47:04,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg485c31c2-616e-4adb-b1ad-facf8817148b/GCF_014773395.1_ASM1477339v1_genomic.fna.gz --refList GCF_014773395.1_ASM1477339v1_genomic.fna/target_genomes.txt --output GCF_014773395.1_ASM1477339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:19,644] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:19,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5058f238-b6ec-4d55-86e6-4a45a4006b2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:19,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5058f238-b6ec-4d55-86e6-4a45a4006b2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:19,651] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:47:19,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:47:19,651] [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
Neiella marina	strain=CGMCC 1.10130	GCA_014636195.1	508461	508461	type	True	84.892	932	1418	95	below_threshold
Neiella marina	strain=J221	GCA_002165625.1	508461	508461	type	True	84.8028	945	1418	95	below_threshold
Neiella holothuriorum	strain=126	GCA_019457915.1	2870530	2870530	type	True	80.0067	468	1418	95	below_threshold
Echinimonas agarilytica	strain=KMM 6351	GCA_023703465.1	1215918	1215918	type	True	78.9955	192	1418	95	below_threshold
Thaumasiovibrio occultus	strain=C4II189	GCA_019703815.1	1891184	1891184	type	True	76.8188	55	1418	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	76.4041	53	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:19,653] [INFO] DFAST Taxonomy check result was written to GCF_014773395.1_ASM1477339v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:19,654] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:19,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:19,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5058f238-b6ec-4d55-86e6-4a45a4006b2f/dqc_reference/checkm_data
[2024-01-25 19:47:19,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:19,698] [INFO] Task started: CheckM
[2024-01-25 19:47:19,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773395.1_ASM1477339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773395.1_ASM1477339v1_genomic.fna/checkm_input GCF_014773395.1_ASM1477339v1_genomic.fna/checkm_result
[2024-01-25 19:47:55,334] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:55,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:55,368] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:55,369] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:55,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773395.1_ASM1477339v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:55,369] [INFO] Task started: Blastn
[2024-01-25 19:47:55,369] [INFO] Running command: blastn -query GCF_014773395.1_ASM1477339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5058f238-b6ec-4d55-86e6-4a45a4006b2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773395.1_ASM1477339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:56,604] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:56,606] [INFO] Selected 24 target genomes.
[2024-01-25 19:47:56,607] [INFO] Target genome list was writen to GCF_014773395.1_ASM1477339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:56,647] [INFO] Task started: fastANI
[2024-01-25 19:47:56,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg485c31c2-616e-4adb-b1ad-facf8817148b/GCF_014773395.1_ASM1477339v1_genomic.fna.gz --refList GCF_014773395.1_ASM1477339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014773395.1_ASM1477339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:13,507] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:13,511] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:13,511] [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_014773395.1	s__Neiella sp014773395	100.0	1413	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Neiellaceae;g__Neiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002165625.1	s__Neiella marina	84.7914	947	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Neiellaceae;g__Neiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000429485.1	s__Aliagarivorans marinus	77.4317	78	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Aliagarivorans	95.1281	N/A	N/A	N/A	N/A	1	-
GCF_005116665.1	s__Ferrimonas sp005116665	76.9837	59	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157795.1	s__Thaumasiovibrio occultus	76.8771	53	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Thaumasiovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:13,513] [INFO] GTDB search result was written to GCF_014773395.1_ASM1477339v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:13,513] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:13,516] [INFO] DFAST_QC result json was written to GCF_014773395.1_ASM1477339v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:13,516] [INFO] DFAST_QC completed!
[2024-01-25 19:48:13,516] [INFO] Total running time: 0h1m23s