[2024-01-24 13:37:13,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg71c29f7f-8999-401a-b708-77e703d0eabc/dqc_reference
[2024-01-24 13:37:14,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,944] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg9553a355-8031-47f6-9235-0192d63ad63a/GCF_020552705.1_ASM2055270v1_genomic.fna.gz | prodigal -d GCF_020552705.1_ASM2055270v1_genomic.fna/cds.fna -a GCF_020552705.1_ASM2055270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:26,368] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:26,369] [INFO] Task started: HMMsearch
[2024-01-24 13:37:26,369] [INFO] Running command: hmmsearch --tblout GCF_020552705.1_ASM2055270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71c29f7f-8999-401a-b708-77e703d0eabc/dqc_reference/reference_markers.hmm GCF_020552705.1_ASM2055270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:26,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:26,665] [INFO] Found 6/6 markers.
[2024-01-24 13:37:26,706] [INFO] Query marker FASTA was written to GCF_020552705.1_ASM2055270v1_genomic.fna/markers.fasta
[2024-01-24 13:37:26,707] [INFO] Task started: Blastn
[2024-01-24 13:37:26,707] [INFO] Running command: blastn -query GCF_020552705.1_ASM2055270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71c29f7f-8999-401a-b708-77e703d0eabc/dqc_reference/reference_markers.fasta -out GCF_020552705.1_ASM2055270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:27,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:27,430] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:27,431] [INFO] Target genome list was writen to GCF_020552705.1_ASM2055270v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:27,442] [INFO] Task started: fastANI
[2024-01-24 13:37:27,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg9553a355-8031-47f6-9235-0192d63ad63a/GCF_020552705.1_ASM2055270v1_genomic.fna.gz --refList GCF_020552705.1_ASM2055270v1_genomic.fna/target_genomes.txt --output GCF_020552705.1_ASM2055270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:35,216] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71c29f7f-8999-401a-b708-77e703d0eabc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:35,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71c29f7f-8999-401a-b708-77e703d0eabc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:35,227] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:35,227] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:35,227] [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 forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	81.9373	746	1082	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	81.8995	744	1082	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	81.1351	629	1082	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	80.9533	624	1082	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	80.2421	530	1082	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	80.1691	524	1082	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	80.0561	567	1082	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	79.3393	485	1082	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.4511	277	1082	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.4101	261	1082	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	76.4033	51	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,230] [INFO] DFAST Taxonomy check result was written to GCF_020552705.1_ASM2055270v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:35,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:35,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:35,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71c29f7f-8999-401a-b708-77e703d0eabc/dqc_reference/checkm_data
[2024-01-24 13:37:35,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:35,272] [INFO] Task started: CheckM
[2024-01-24 13:37:35,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020552705.1_ASM2055270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020552705.1_ASM2055270v1_genomic.fna/checkm_input GCF_020552705.1_ASM2055270v1_genomic.fna/checkm_result
[2024-01-24 13:38:13,248] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:13,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:13,273] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:13,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:13,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020552705.1_ASM2055270v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:13,275] [INFO] Task started: Blastn
[2024-01-24 13:38:13,275] [INFO] Running command: blastn -query GCF_020552705.1_ASM2055270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71c29f7f-8999-401a-b708-77e703d0eabc/dqc_reference/reference_markers_gtdb.fasta -out GCF_020552705.1_ASM2055270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:14,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:14,146] [INFO] Selected 7 target genomes.
[2024-01-24 13:38:14,146] [INFO] Target genome list was writen to GCF_020552705.1_ASM2055270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:14,158] [INFO] Task started: fastANI
[2024-01-24 13:38:14,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg9553a355-8031-47f6-9235-0192d63ad63a/GCF_020552705.1_ASM2055270v1_genomic.fna.gz --refList GCF_020552705.1_ASM2055270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020552705.1_ASM2055270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:19,202] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:19,212] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:19,212] [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_900105135.1	s__Gramella sp900105135	82.0336	689	1082	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	81.9313	747	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000423065.1	s__Gramella echinicola	81.1425	628	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_003054225.1	s__Gramella gaetbulicola	80.9357	626	1082	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	80.267	528	1082	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	80.1664	525	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889005.1	s__Gramella salexigens	79.1626	420	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:19,215] [INFO] GTDB search result was written to GCF_020552705.1_ASM2055270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:19,216] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:19,219] [INFO] DFAST_QC result json was written to GCF_020552705.1_ASM2055270v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:19,220] [INFO] DFAST_QC completed!
[2024-01-24 13:38:19,220] [INFO] Total running time: 0h1m5s