[2023-06-19 02:08:11,134] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:08:11,135] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:08:11,136] [INFO] DQC Reference Directory: /var/lib/cwl/stga1b49f30-e4d1-44e4-8f3d-6110944585c5/dqc_reference
[2023-06-19 02:08:12,289] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:08:12,290] [INFO] Task started: Prodigal
[2023-06-19 02:08:12,291] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf42fb8f-3eea-4f27-9a3e-fbdde78e0ef8/GCA_013377115.1_ASM1337711v1_genomic.fna.gz | prodigal -d GCA_013377115.1_ASM1337711v1_genomic.fna/cds.fna -a GCA_013377115.1_ASM1337711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:08:25,814] [INFO] Task succeeded: Prodigal
[2023-06-19 02:08:25,814] [INFO] Task started: HMMsearch
[2023-06-19 02:08:25,814] [INFO] Running command: hmmsearch --tblout GCA_013377115.1_ASM1337711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1b49f30-e4d1-44e4-8f3d-6110944585c5/dqc_reference/reference_markers.hmm GCA_013377115.1_ASM1337711v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:08:26,025] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:08:26,026] [INFO] Found 6/6 markers.
[2023-06-19 02:08:26,096] [INFO] Query marker FASTA was written to GCA_013377115.1_ASM1337711v1_genomic.fna/markers.fasta
[2023-06-19 02:08:26,096] [INFO] Task started: Blastn
[2023-06-19 02:08:26,096] [INFO] Running command: blastn -query GCA_013377115.1_ASM1337711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1b49f30-e4d1-44e4-8f3d-6110944585c5/dqc_reference/reference_markers.fasta -out GCA_013377115.1_ASM1337711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:08:26,687] [INFO] Task succeeded: Blastn
[2023-06-19 02:08:26,692] [INFO] Selected 28 target genomes.
[2023-06-19 02:08:26,693] [INFO] Target genome list was writen to GCA_013377115.1_ASM1337711v1_genomic.fna/target_genomes.txt
[2023-06-19 02:08:26,696] [INFO] Task started: fastANI
[2023-06-19 02:08:26,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf42fb8f-3eea-4f27-9a3e-fbdde78e0ef8/GCA_013377115.1_ASM1337711v1_genomic.fna.gz --refList GCA_013377115.1_ASM1337711v1_genomic.fna/target_genomes.txt --output GCA_013377115.1_ASM1337711v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:08:42,589] [INFO] Task succeeded: fastANI
[2023-06-19 02:08:42,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1b49f30-e4d1-44e4-8f3d-6110944585c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:08:42,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1b49f30-e4d1-44e4-8f3d-6110944585c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:08:42,597] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:08:42,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:08:42,597] [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
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	75.4797	50	1192	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	74.9077	50	1192	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	74.7581	52	1192	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	74.7568	50	1192	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:08:42,599] [INFO] DFAST Taxonomy check result was written to GCA_013377115.1_ASM1337711v1_genomic.fna/tc_result.tsv
[2023-06-19 02:08:42,600] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:08:42,600] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:08:42,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1b49f30-e4d1-44e4-8f3d-6110944585c5/dqc_reference/checkm_data
[2023-06-19 02:08:42,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:08:42,639] [INFO] Task started: CheckM
[2023-06-19 02:08:42,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013377115.1_ASM1337711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013377115.1_ASM1337711v1_genomic.fna/checkm_input GCA_013377115.1_ASM1337711v1_genomic.fna/checkm_result
[2023-06-19 02:09:24,850] [INFO] Task succeeded: CheckM
[2023-06-19 02:09:24,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:09:24,869] [INFO] ===== Completeness check finished =====
[2023-06-19 02:09:24,869] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:09:24,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013377115.1_ASM1337711v1_genomic.fna/markers.fasta)
[2023-06-19 02:09:24,870] [INFO] Task started: Blastn
[2023-06-19 02:09:24,870] [INFO] Running command: blastn -query GCA_013377115.1_ASM1337711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1b49f30-e4d1-44e4-8f3d-6110944585c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_013377115.1_ASM1337711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:09:25,637] [INFO] Task succeeded: Blastn
[2023-06-19 02:09:25,641] [INFO] Selected 29 target genomes.
[2023-06-19 02:09:25,641] [INFO] Target genome list was writen to GCA_013377115.1_ASM1337711v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:09:25,651] [INFO] Task started: fastANI
[2023-06-19 02:09:25,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf42fb8f-3eea-4f27-9a3e-fbdde78e0ef8/GCA_013377115.1_ASM1337711v1_genomic.fna.gz --refList GCA_013377115.1_ASM1337711v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013377115.1_ASM1337711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:09:40,567] [INFO] Task succeeded: fastANI
[2023-06-19 02:09:40,579] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:09:40,579] [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_013377115.1	s__Cfx2-01 sp013377115	100.0	1179	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CG2-30-32-10;g__Cfx2-01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903899825.1	s__JACABE01 sp903899825	75.839	58	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JACABE01;g__JACABE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377005.1	s__JACABE01 sp013377005	75.6432	82	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JACABE01;g__JACABE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913285.1	s__CAIWKO01 sp903913285	75.5759	52	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CAIWKO01;g__CAIWKO01	95.0	99.97	99.95	0.97	0.97	3	-
GCA_903922465.1	s__CAIXTV01 sp903922465	75.3814	55	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CAIXTV01;g__CAIXTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903936865.1	s__JACABE01 sp903936865	75.3143	82	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JACABE01;g__JACABE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696965.1	s__JACCXN01 sp013696965	75.1564	53	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__JACCXN01;g__JACCXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001769505.1	s__GWF2-33-38 sp001769505	75.0931	52	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWF2-33-38;g__GWF2-33-38	95.0	99.92	99.84	0.98	0.98	4	-
GCF_004121075.1	s__Lutibacter sp004121075	75.0866	54	1192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:09:40,581] [INFO] GTDB search result was written to GCA_013377115.1_ASM1337711v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:09:40,582] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:09:40,585] [INFO] DFAST_QC result json was written to GCA_013377115.1_ASM1337711v1_genomic.fna/dqc_result.json
[2023-06-19 02:09:40,585] [INFO] DFAST_QC completed!
[2023-06-19 02:09:40,585] [INFO] Total running time: 0h1m29s