[2024-01-24 13:40:46,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg90516bee-9cb0-44c3-8c50-88d541cbef93/dqc_reference
[2024-01-24 13:40:47,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,831] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,831] [INFO] Running command: gunzip -c /var/lib/cwl/stgeed3c7cb-4e54-4f9f-a7e3-7a9d1bb055b4/GCF_002312815.1_ASM231281v1_genomic.fna.gz | prodigal -d GCF_002312815.1_ASM231281v1_genomic.fna/cds.fna -a GCF_002312815.1_ASM231281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,502] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,502] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,502] [INFO] Running command: hmmsearch --tblout GCF_002312815.1_ASM231281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90516bee-9cb0-44c3-8c50-88d541cbef93/dqc_reference/reference_markers.hmm GCF_002312815.1_ASM231281v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,770] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,810] [INFO] Query marker FASTA was written to GCF_002312815.1_ASM231281v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,810] [INFO] Task started: Blastn
[2024-01-24 13:40:58,810] [INFO] Running command: blastn -query GCF_002312815.1_ASM231281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90516bee-9cb0-44c3-8c50-88d541cbef93/dqc_reference/reference_markers.fasta -out GCF_002312815.1_ASM231281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,576] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,580] [INFO] Selected 26 target genomes.
[2024-01-24 13:40:59,581] [INFO] Target genome list was writen to GCF_002312815.1_ASM231281v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,617] [INFO] Task started: fastANI
[2024-01-24 13:40:59,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed3c7cb-4e54-4f9f-a7e3-7a9d1bb055b4/GCF_002312815.1_ASM231281v1_genomic.fna.gz --refList GCF_002312815.1_ASM231281v1_genomic.fna/target_genomes.txt --output GCF_002312815.1_ASM231281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,770] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90516bee-9cb0-44c3-8c50-88d541cbef93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90516bee-9cb0-44c3-8c50-88d541cbef93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,782] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:14,782] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:14,782] [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
Agaribacterium haliotis	strain=feces2	GCA_002312815.1	2013869	2013869	type	True	100.0	1376	1379	95	conclusive
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	77.1319	54	1379	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	77.0178	53	1379	95	below_threshold
Teredinibacter franksiae	strain=Bsc2	GCA_014218805.1	2761453	2761453	type	True	76.8724	50	1379	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.7666	53	1379	95	below_threshold
Aestuariicella hydrocarbonica	strain=JCM 30134	GCA_011602365.1	1470433	1470433	type	True	76.7166	50	1379	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.5259	60	1379	95	below_threshold
Teredinibacter turnerae	strain=T7902	GCA_000379165.1	2426	2426	type	True	76.3735	65	1379	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	76.1677	50	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,784] [INFO] DFAST Taxonomy check result was written to GCF_002312815.1_ASM231281v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90516bee-9cb0-44c3-8c50-88d541cbef93/dqc_reference/checkm_data
[2024-01-24 13:41:14,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,834] [INFO] Task started: CheckM
[2024-01-24 13:41:14,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002312815.1_ASM231281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002312815.1_ASM231281v1_genomic.fna/checkm_input GCF_002312815.1_ASM231281v1_genomic.fna/checkm_result
[2024-01-24 13:41:50,499] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:50,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,528] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:50,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:50,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002312815.1_ASM231281v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:50,529] [INFO] Task started: Blastn
[2024-01-24 13:41:50,530] [INFO] Running command: blastn -query GCF_002312815.1_ASM231281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90516bee-9cb0-44c3-8c50-88d541cbef93/dqc_reference/reference_markers_gtdb.fasta -out GCF_002312815.1_ASM231281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,859] [INFO] Selected 26 target genomes.
[2024-01-24 13:41:51,859] [INFO] Target genome list was writen to GCF_002312815.1_ASM231281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:52,036] [INFO] Task started: fastANI
[2024-01-24 13:41:52,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed3c7cb-4e54-4f9f-a7e3-7a9d1bb055b4/GCF_002312815.1_ASM231281v1_genomic.fna.gz --refList GCF_002312815.1_ASM231281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002312815.1_ASM231281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:08,893] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:08,904] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:08,905] [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_002312815.1	s__Agaribacterium haliotis	100.0	1376	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agaribacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003265435.1	s__Agaribacterium sp003265435	77.2945	116	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agaribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218805.1	s__Teredinibacter franksiae	76.8724	50	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903625.1	s__Microbulbifer sp009903625	76.8174	51	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	76.6906	54	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377745.1	s__Gilvimarinus chinensis	76.6761	56	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023025.1	s__Teredinibacter turnerae_B	76.5438	65	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	98.16	98.08	0.93	0.93	4	-
GCA_003634075.1	s__Teredinibacter sp003634075	76.5279	90	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:08,907] [INFO] GTDB search result was written to GCF_002312815.1_ASM231281v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:08,907] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:08,910] [INFO] DFAST_QC result json was written to GCF_002312815.1_ASM231281v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:08,910] [INFO] DFAST_QC completed!
[2024-01-24 13:42:08,910] [INFO] Total running time: 0h1m22s