[2024-01-25 20:15:35,749] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:35,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:35,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg6df4969f-87ef-46f8-83ab-1630a5f02fa7/dqc_reference
[2024-01-25 20:15:37,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:37,022] [INFO] Task started: Prodigal
[2024-01-25 20:15:37,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg14f66fca-bc19-4469-89c7-90504d6615c4/GCF_000423045.1_ASM42304v1_genomic.fna.gz | prodigal -d GCF_000423045.1_ASM42304v1_genomic.fna/cds.fna -a GCF_000423045.1_ASM42304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:47,854] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:47,855] [INFO] Task started: HMMsearch
[2024-01-25 20:15:47,855] [INFO] Running command: hmmsearch --tblout GCF_000423045.1_ASM42304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6df4969f-87ef-46f8-83ab-1630a5f02fa7/dqc_reference/reference_markers.hmm GCF_000423045.1_ASM42304v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:48,101] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:48,102] [INFO] Found 6/6 markers.
[2024-01-25 20:15:48,129] [INFO] Query marker FASTA was written to GCF_000423045.1_ASM42304v1_genomic.fna/markers.fasta
[2024-01-25 20:15:48,129] [INFO] Task started: Blastn
[2024-01-25 20:15:48,129] [INFO] Running command: blastn -query GCF_000423045.1_ASM42304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df4969f-87ef-46f8-83ab-1630a5f02fa7/dqc_reference/reference_markers.fasta -out GCF_000423045.1_ASM42304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:48,755] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:48,758] [INFO] Selected 14 target genomes.
[2024-01-25 20:15:48,758] [INFO] Target genome list was writen to GCF_000423045.1_ASM42304v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:48,763] [INFO] Task started: fastANI
[2024-01-25 20:15:48,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg14f66fca-bc19-4469-89c7-90504d6615c4/GCF_000423045.1_ASM42304v1_genomic.fna.gz --refList GCF_000423045.1_ASM42304v1_genomic.fna/target_genomes.txt --output GCF_000423045.1_ASM42304v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:57,815] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:57,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6df4969f-87ef-46f8-83ab-1630a5f02fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:57,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6df4969f-87ef-46f8-83ab-1630a5f02fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:57,824] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:57,824] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:57,824] [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
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	100.0	1083	1084	95	conclusive
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	79.5343	431	1084	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	79.2049	381	1084	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	79.0208	366	1084	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	78.9356	395	1084	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	78.9156	407	1084	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	78.8425	373	1084	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	78.8024	386	1084	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	78.2056	319	1084	95	below_threshold
Gramella fulva	strain=SH35	GCA_003024155.1	2126553	2126553	type	True	77.7827	261	1084	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.2372	180	1084	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.1536	200	1084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:57,825] [INFO] DFAST Taxonomy check result was written to GCF_000423045.1_ASM42304v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:57,826] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:57,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:57,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6df4969f-87ef-46f8-83ab-1630a5f02fa7/dqc_reference/checkm_data
[2024-01-25 20:15:57,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:57,860] [INFO] Task started: CheckM
[2024-01-25 20:15:57,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423045.1_ASM42304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423045.1_ASM42304v1_genomic.fna/checkm_input GCF_000423045.1_ASM42304v1_genomic.fna/checkm_result
[2024-01-25 20:16:32,142] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:32,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:32,163] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:32,163] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:32,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423045.1_ASM42304v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:32,164] [INFO] Task started: Blastn
[2024-01-25 20:16:32,164] [INFO] Running command: blastn -query GCF_000423045.1_ASM42304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df4969f-87ef-46f8-83ab-1630a5f02fa7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423045.1_ASM42304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:33,000] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:33,003] [INFO] Selected 8 target genomes.
[2024-01-25 20:16:33,003] [INFO] Target genome list was writen to GCF_000423045.1_ASM42304v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:33,007] [INFO] Task started: fastANI
[2024-01-25 20:16:33,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg14f66fca-bc19-4469-89c7-90504d6615c4/GCF_000423045.1_ASM42304v1_genomic.fna.gz --refList GCF_000423045.1_ASM42304v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423045.1_ASM42304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:38,725] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:38,731] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:38,732] [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_000423045.1	s__Gramella portivictoriae	100.0	1083	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006714895.1	s__Gramella sp006714895	85.6945	871	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054225.1	s__Gramella gaetbulicola	79.5554	429	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	79.21	383	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_900105135.1	s__Gramella sp900105135	79.1864	382	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	79.0264	366	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	78.9009	407	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009735585.1	s__Gramella aestuarii	78.8059	386	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:38,734] [INFO] GTDB search result was written to GCF_000423045.1_ASM42304v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:38,734] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:38,737] [INFO] DFAST_QC result json was written to GCF_000423045.1_ASM42304v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:38,737] [INFO] DFAST_QC completed!
[2024-01-25 20:16:38,737] [INFO] Total running time: 0h1m3s