[2023-06-28 09:02:57,040] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:02:57,042] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:02:57,044] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf8868d7-59fe-4d7e-9246-0415668b5c89/dqc_reference
[2023-06-28 09:02:58,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:02:58,439] [INFO] Task started: Prodigal
[2023-06-28 09:02:58,439] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c84c144-514e-4d95-9de5-6b74f24dcea7/GCA_002708475.1_ASM270847v1_genomic.fna.gz | prodigal -d GCA_002708475.1_ASM270847v1_genomic.fna/cds.fna -a GCA_002708475.1_ASM270847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:03:03,678] [INFO] Task succeeded: Prodigal
[2023-06-28 09:03:03,678] [INFO] Task started: HMMsearch
[2023-06-28 09:03:03,678] [INFO] Running command: hmmsearch --tblout GCA_002708475.1_ASM270847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf8868d7-59fe-4d7e-9246-0415668b5c89/dqc_reference/reference_markers.hmm GCA_002708475.1_ASM270847v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:03:03,951] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:03:03,952] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9c84c144-514e-4d95-9de5-6b74f24dcea7/GCA_002708475.1_ASM270847v1_genomic.fna.gz]
[2023-06-28 09:03:03,987] [INFO] Query marker FASTA was written to GCA_002708475.1_ASM270847v1_genomic.fna/markers.fasta
[2023-06-28 09:03:03,987] [INFO] Task started: Blastn
[2023-06-28 09:03:03,987] [INFO] Running command: blastn -query GCA_002708475.1_ASM270847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf8868d7-59fe-4d7e-9246-0415668b5c89/dqc_reference/reference_markers.fasta -out GCA_002708475.1_ASM270847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:03:04,509] [INFO] Task succeeded: Blastn
[2023-06-28 09:03:04,513] [INFO] Selected 20 target genomes.
[2023-06-28 09:03:04,513] [INFO] Target genome list was writen to GCA_002708475.1_ASM270847v1_genomic.fna/target_genomes.txt
[2023-06-28 09:03:04,520] [INFO] Task started: fastANI
[2023-06-28 09:03:04,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c84c144-514e-4d95-9de5-6b74f24dcea7/GCA_002708475.1_ASM270847v1_genomic.fna.gz --refList GCA_002708475.1_ASM270847v1_genomic.fna/target_genomes.txt --output GCA_002708475.1_ASM270847v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:03:17,608] [INFO] Task succeeded: fastANI
[2023-06-28 09:03:17,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf8868d7-59fe-4d7e-9246-0415668b5c89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:03:17,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf8868d7-59fe-4d7e-9246-0415668b5c89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:03:17,613] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:03:17,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 09:03:17,613] [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
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	76.7957	87	844	95	below_threshold
Bermanella marisrubri	strain=RED65	GCA_012295615.1	207949	207949	type	True	76.2581	50	844	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 09:03:17,616] [INFO] DFAST Taxonomy check result was written to GCA_002708475.1_ASM270847v1_genomic.fna/tc_result.tsv
[2023-06-28 09:03:17,616] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:03:17,616] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:03:17,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf8868d7-59fe-4d7e-9246-0415668b5c89/dqc_reference/checkm_data
[2023-06-28 09:03:17,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:03:17,647] [INFO] Task started: CheckM
[2023-06-28 09:03:17,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708475.1_ASM270847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708475.1_ASM270847v1_genomic.fna/checkm_input GCA_002708475.1_ASM270847v1_genomic.fna/checkm_result
[2023-06-28 09:03:40,919] [INFO] Task succeeded: CheckM
[2023-06-28 09:03:40,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 09:03:40,944] [INFO] ===== Completeness check finished =====
[2023-06-28 09:03:40,945] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:03:40,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708475.1_ASM270847v1_genomic.fna/markers.fasta)
[2023-06-28 09:03:40,945] [INFO] Task started: Blastn
[2023-06-28 09:03:40,946] [INFO] Running command: blastn -query GCA_002708475.1_ASM270847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf8868d7-59fe-4d7e-9246-0415668b5c89/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708475.1_ASM270847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:03:41,476] [INFO] Task succeeded: Blastn
[2023-06-28 09:03:41,480] [INFO] Selected 10 target genomes.
[2023-06-28 09:03:41,480] [INFO] Target genome list was writen to GCA_002708475.1_ASM270847v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:03:41,489] [INFO] Task started: fastANI
[2023-06-28 09:03:41,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c84c144-514e-4d95-9de5-6b74f24dcea7/GCA_002708475.1_ASM270847v1_genomic.fna.gz --refList GCA_002708475.1_ASM270847v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708475.1_ASM270847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:03:47,819] [INFO] Task succeeded: fastANI
[2023-06-28 09:03:47,829] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 09:03:47,830] [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_002708475.1	s__Oleispira sp002708475	100.0	839	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	98.91	98.91	0.78	0.78	2	conclusive
GCA_000967895.1	s__Oleispira antarctica	80.6637	422	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	99.07	99.06	0.98	0.98	3	-
GCA_002632185.1	s__Oleispira sp002632185	80.4106	245	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765295.1	s__Oleispira sp016765295	80.2796	334	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733645.1	s__Oleibacter sp002733645	76.7412	56	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	97.97	97.97	0.87	0.87	2	-
GCF_012295615.1	s__Bermanella marisrubri	76.2581	50	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-28 09:03:47,832] [INFO] GTDB search result was written to GCA_002708475.1_ASM270847v1_genomic.fna/result_gtdb.tsv
[2023-06-28 09:03:47,832] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:03:47,835] [INFO] DFAST_QC result json was written to GCA_002708475.1_ASM270847v1_genomic.fna/dqc_result.json
[2023-06-28 09:03:47,835] [INFO] DFAST_QC completed!
[2023-06-28 09:03:47,836] [INFO] Total running time: 0h0m51s