[2024-01-24 13:36:31,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,113] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaee457e-0540-433f-bbe4-f889a9d9db76/dqc_reference
[2024-01-24 13:36:32,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,502] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg310bdc41-ac37-4a7e-a894-a9593e6b8c2e/GCF_000265405.1_ASM26540v1_genomic.fna.gz | prodigal -d GCF_000265405.1_ASM26540v1_genomic.fna/cds.fna -a GCF_000265405.1_ASM26540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:50,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:50,143] [INFO] Task started: HMMsearch
[2024-01-24 13:36:50,143] [INFO] Running command: hmmsearch --tblout GCF_000265405.1_ASM26540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaee457e-0540-433f-bbe4-f889a9d9db76/dqc_reference/reference_markers.hmm GCF_000265405.1_ASM26540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:50,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:50,427] [INFO] Found 6/6 markers.
[2024-01-24 13:36:50,466] [INFO] Query marker FASTA was written to GCF_000265405.1_ASM26540v1_genomic.fna/markers.fasta
[2024-01-24 13:36:50,466] [INFO] Task started: Blastn
[2024-01-24 13:36:50,467] [INFO] Running command: blastn -query GCF_000265405.1_ASM26540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaee457e-0540-433f-bbe4-f889a9d9db76/dqc_reference/reference_markers.fasta -out GCF_000265405.1_ASM26540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:51,082] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:51,086] [INFO] Selected 15 target genomes.
[2024-01-24 13:36:51,087] [INFO] Target genome list was writen to GCF_000265405.1_ASM26540v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:51,109] [INFO] Task started: fastANI
[2024-01-24 13:36:51,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg310bdc41-ac37-4a7e-a894-a9593e6b8c2e/GCF_000265405.1_ASM26540v1_genomic.fna.gz --refList GCF_000265405.1_ASM26540v1_genomic.fna/target_genomes.txt --output GCF_000265405.1_ASM26540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:02,333] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:02,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaee457e-0540-433f-bbe4-f889a9d9db76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:02,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaee457e-0540-433f-bbe4-f889a9d9db76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:02,345] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:02,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:02,345] [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 baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	100.0	1398	1398	95	conclusive
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	86.7668	977	1398	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	86.7484	978	1398	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	80.8712	554	1398	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	80.7968	549	1398	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	78.193	332	1398	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	78.0494	130	1398	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_003254355.1	57028	57028	type	True	76.4398	101	1398	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	76.4374	104	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:02,347] [INFO] DFAST Taxonomy check result was written to GCF_000265405.1_ASM26540v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:02,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:02,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:02,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaee457e-0540-433f-bbe4-f889a9d9db76/dqc_reference/checkm_data
[2024-01-24 13:37:02,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:02,392] [INFO] Task started: CheckM
[2024-01-24 13:37:02,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000265405.1_ASM26540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000265405.1_ASM26540v1_genomic.fna/checkm_input GCF_000265405.1_ASM26540v1_genomic.fna/checkm_result
[2024-01-24 13:37:58,115] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:58,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,134] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:58,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:58,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000265405.1_ASM26540v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:58,136] [INFO] Task started: Blastn
[2024-01-24 13:37:58,136] [INFO] Running command: blastn -query GCF_000265405.1_ASM26540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaee457e-0540-433f-bbe4-f889a9d9db76/dqc_reference/reference_markers_gtdb.fasta -out GCF_000265405.1_ASM26540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:58,948] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:58,953] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:58,953] [INFO] Target genome list was writen to GCF_000265405.1_ASM26540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:58,974] [INFO] Task started: fastANI
[2024-01-24 13:37:58,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg310bdc41-ac37-4a7e-a894-a9593e6b8c2e/GCF_000265405.1_ASM26540v1_genomic.fna.gz --refList GCF_000265405.1_ASM26540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000265405.1_ASM26540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:13,750] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:13,771] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:13,771] [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_000265405.1	s__Belliella baltica	100.0	1398	1398	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_014637795.1	s__Belliella aquatica	86.7542	978	1398	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	80.8851	551	1398	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	80.7909	550	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	79.4329	214	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	79.2406	231	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	77.4454	126	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	77.2667	200	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381545.1	s__Rhodonellum psychrophilum	76.9105	181	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
GCF_017051705.1	s__Algoriphagus lutimaris	76.9077	119	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	76.8574	175	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	76.8571	192	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	76.4374	104	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:13,773] [INFO] GTDB search result was written to GCF_000265405.1_ASM26540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:13,773] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:13,776] [INFO] DFAST_QC result json was written to GCF_000265405.1_ASM26540v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:13,777] [INFO] DFAST_QC completed!
[2024-01-24 13:38:13,777] [INFO] Total running time: 0h1m43s