[2024-01-25 20:07:20,454] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:20,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:20,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg888686db-2ae9-4c59-a9b0-788ec4c6a629/dqc_reference
[2024-01-25 20:07:21,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:21,596] [INFO] Task started: Prodigal
[2024-01-25 20:07:21,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cbc6f52-36fe-4cbf-bc2a-d94bf6df3116/GCF_022489035.1_ASM2248903v1_genomic.fna.gz | prodigal -d GCF_022489035.1_ASM2248903v1_genomic.fna/cds.fna -a GCF_022489035.1_ASM2248903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:31,926] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:31,926] [INFO] Task started: HMMsearch
[2024-01-25 20:07:31,926] [INFO] Running command: hmmsearch --tblout GCF_022489035.1_ASM2248903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg888686db-2ae9-4c59-a9b0-788ec4c6a629/dqc_reference/reference_markers.hmm GCF_022489035.1_ASM2248903v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:32,152] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:32,153] [INFO] Found 6/6 markers.
[2024-01-25 20:07:32,181] [INFO] Query marker FASTA was written to GCF_022489035.1_ASM2248903v1_genomic.fna/markers.fasta
[2024-01-25 20:07:32,181] [INFO] Task started: Blastn
[2024-01-25 20:07:32,182] [INFO] Running command: blastn -query GCF_022489035.1_ASM2248903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg888686db-2ae9-4c59-a9b0-788ec4c6a629/dqc_reference/reference_markers.fasta -out GCF_022489035.1_ASM2248903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:32,782] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:32,785] [INFO] Selected 11 target genomes.
[2024-01-25 20:07:32,785] [INFO] Target genome list was writen to GCF_022489035.1_ASM2248903v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:32,790] [INFO] Task started: fastANI
[2024-01-25 20:07:32,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cbc6f52-36fe-4cbf-bc2a-d94bf6df3116/GCF_022489035.1_ASM2248903v1_genomic.fna.gz --refList GCF_022489035.1_ASM2248903v1_genomic.fna/target_genomes.txt --output GCF_022489035.1_ASM2248903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:40,462] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:40,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg888686db-2ae9-4c59-a9b0-788ec4c6a629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:40,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg888686db-2ae9-4c59-a9b0-788ec4c6a629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:40,471] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:40,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:40,471] [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 lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	100.0	1139	1141	95	conclusive
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	80.8255	652	1141	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	80.7512	600	1141	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	80.4481	631	1141	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	80.1344	534	1141	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	79.8308	540	1141	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	79.7611	558	1141	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	79.2882	446	1141	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.3162	207	1141	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	76.915	52	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:40,472] [INFO] DFAST Taxonomy check result was written to GCF_022489035.1_ASM2248903v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:40,473] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:40,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:40,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg888686db-2ae9-4c59-a9b0-788ec4c6a629/dqc_reference/checkm_data
[2024-01-25 20:07:40,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:40,509] [INFO] Task started: CheckM
[2024-01-25 20:07:40,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022489035.1_ASM2248903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022489035.1_ASM2248903v1_genomic.fna/checkm_input GCF_022489035.1_ASM2248903v1_genomic.fna/checkm_result
[2024-01-25 20:08:13,216] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:13,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:13,231] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:13,231] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:13,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022489035.1_ASM2248903v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:13,232] [INFO] Task started: Blastn
[2024-01-25 20:08:13,232] [INFO] Running command: blastn -query GCF_022489035.1_ASM2248903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg888686db-2ae9-4c59-a9b0-788ec4c6a629/dqc_reference/reference_markers_gtdb.fasta -out GCF_022489035.1_ASM2248903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:14,059] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:14,061] [INFO] Selected 8 target genomes.
[2024-01-25 20:08:14,062] [INFO] Target genome list was writen to GCF_022489035.1_ASM2248903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:14,067] [INFO] Task started: fastANI
[2024-01-25 20:08:14,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cbc6f52-36fe-4cbf-bc2a-d94bf6df3116/GCF_022489035.1_ASM2248903v1_genomic.fna.gz --refList GCF_022489035.1_ASM2248903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022489035.1_ASM2248903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:19,655] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:19,661] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:08:19,661] [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_003054225.1	s__Gramella gaetbulicola	80.8044	655	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	80.76	600	1141	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	80.4404	630	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_007050985.1	s__Gramella sabulilitoris	80.1357	532	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105135.1	s__Gramella sp900105135	79.912	517	1141	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	79.831	540	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004332155.1	s__Gramella sp004332155	79.3483	409	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006714895.1	s__Gramella sp006714895	79.0719	389	1141	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 20:08:19,662] [INFO] GTDB search result was written to GCF_022489035.1_ASM2248903v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:19,663] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:19,665] [INFO] DFAST_QC result json was written to GCF_022489035.1_ASM2248903v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:19,665] [INFO] DFAST_QC completed!
[2024-01-25 20:08:19,665] [INFO] Total running time: 0h0m59s