[2024-01-25 18:50:20,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:20,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:20,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg9864cd77-bf26-4066-8ab4-221b9d47ef42/dqc_reference
[2024-01-25 18:50:21,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:21,674] [INFO] Task started: Prodigal
[2024-01-25 18:50:21,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg5add01a6-e49b-45d3-8d08-8fb1c0a38d4b/GCF_014637795.1_ASM1463779v1_genomic.fna.gz | prodigal -d GCF_014637795.1_ASM1463779v1_genomic.fna/cds.fna -a GCF_014637795.1_ASM1463779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:37,538] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:37,539] [INFO] Task started: HMMsearch
[2024-01-25 18:50:37,539] [INFO] Running command: hmmsearch --tblout GCF_014637795.1_ASM1463779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9864cd77-bf26-4066-8ab4-221b9d47ef42/dqc_reference/reference_markers.hmm GCF_014637795.1_ASM1463779v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:37,913] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:37,914] [INFO] Found 6/6 markers.
[2024-01-25 18:50:37,969] [INFO] Query marker FASTA was written to GCF_014637795.1_ASM1463779v1_genomic.fna/markers.fasta
[2024-01-25 18:50:37,970] [INFO] Task started: Blastn
[2024-01-25 18:50:37,970] [INFO] Running command: blastn -query GCF_014637795.1_ASM1463779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9864cd77-bf26-4066-8ab4-221b9d47ef42/dqc_reference/reference_markers.fasta -out GCF_014637795.1_ASM1463779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:38,576] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:38,579] [INFO] Selected 8 target genomes.
[2024-01-25 18:50:38,579] [INFO] Target genome list was writen to GCF_014637795.1_ASM1463779v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:38,586] [INFO] Task started: fastANI
[2024-01-25 18:50:38,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg5add01a6-e49b-45d3-8d08-8fb1c0a38d4b/GCF_014637795.1_ASM1463779v1_genomic.fna.gz --refList GCF_014637795.1_ASM1463779v1_genomic.fna/target_genomes.txt --output GCF_014637795.1_ASM1463779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:46,414] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:46,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9864cd77-bf26-4066-8ab4-221b9d47ef42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:46,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9864cd77-bf26-4066-8ab4-221b9d47ef42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:46,421] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:50:46,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:46,421] [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
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	100.0	1514	1516	95	conclusive
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	99.9917	1505	1516	95	conclusive
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	86.6559	982	1516	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	81.0394	532	1516	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	79.1797	492	1516	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	77.0754	227	1516	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.6066	121	1516	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	76.5468	121	1516	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:46,423] [INFO] DFAST Taxonomy check result was written to GCF_014637795.1_ASM1463779v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:46,424] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:46,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:46,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9864cd77-bf26-4066-8ab4-221b9d47ef42/dqc_reference/checkm_data
[2024-01-25 18:50:46,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:46,470] [INFO] Task started: CheckM
[2024-01-25 18:50:46,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637795.1_ASM1463779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637795.1_ASM1463779v1_genomic.fna/checkm_input GCF_014637795.1_ASM1463779v1_genomic.fna/checkm_result
[2024-01-25 18:51:34,554] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:34,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:34,586] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:34,586] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:34,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637795.1_ASM1463779v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:34,586] [INFO] Task started: Blastn
[2024-01-25 18:51:34,586] [INFO] Running command: blastn -query GCF_014637795.1_ASM1463779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9864cd77-bf26-4066-8ab4-221b9d47ef42/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637795.1_ASM1463779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:35,439] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:35,444] [INFO] Selected 13 target genomes.
[2024-01-25 18:51:35,444] [INFO] Target genome list was writen to GCF_014637795.1_ASM1463779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:35,457] [INFO] Task started: fastANI
[2024-01-25 18:51:35,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg5add01a6-e49b-45d3-8d08-8fb1c0a38d4b/GCF_014637795.1_ASM1463779v1_genomic.fna.gz --refList GCF_014637795.1_ASM1463779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637795.1_ASM1463779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:46,337] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:46,346] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:46,346] [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_014637795.1	s__Belliella aquatica	100.0	1514	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000265405.1	s__Belliella baltica	86.6392	984	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	81.0393	532	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	79.1832	490	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	77.4253	188	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	77.3083	175	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	77.0649	228	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	76.9097	162	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	76.8628	108	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.8085	131	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007655305.1	s__Algoriphagus sp007655305	76.6066	121	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	76.5304	122	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_002150685.1	s__Algoriphagus antarcticus	76.3727	101	1516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:46,347] [INFO] GTDB search result was written to GCF_014637795.1_ASM1463779v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:46,348] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:46,351] [INFO] DFAST_QC result json was written to GCF_014637795.1_ASM1463779v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:46,351] [INFO] DFAST_QC completed!
[2024-01-25 18:51:46,352] [INFO] Total running time: 0h1m26s