[2024-01-24 13:40:44,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,208] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg819a530a-7d47-4b5d-bbe4-17969ae6afb9/dqc_reference
[2024-01-24 13:40:45,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,590] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,591] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e3cffdc-4171-4b4c-91c5-dd0184aab6dd/GCF_015476655.1_ASM1547665v1_genomic.fna.gz | prodigal -d GCF_015476655.1_ASM1547665v1_genomic.fna/cds.fna -a GCF_015476655.1_ASM1547665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:15,547] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:15,548] [INFO] Task started: HMMsearch
[2024-01-24 13:41:15,548] [INFO] Running command: hmmsearch --tblout GCF_015476655.1_ASM1547665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg819a530a-7d47-4b5d-bbe4-17969ae6afb9/dqc_reference/reference_markers.hmm GCF_015476655.1_ASM1547665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:15,902] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:15,903] [INFO] Found 6/6 markers.
[2024-01-24 13:41:15,947] [INFO] Query marker FASTA was written to GCF_015476655.1_ASM1547665v1_genomic.fna/markers.fasta
[2024-01-24 13:41:15,948] [INFO] Task started: Blastn
[2024-01-24 13:41:15,948] [INFO] Running command: blastn -query GCF_015476655.1_ASM1547665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg819a530a-7d47-4b5d-bbe4-17969ae6afb9/dqc_reference/reference_markers.fasta -out GCF_015476655.1_ASM1547665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:16,530] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:16,533] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:16,533] [INFO] Target genome list was writen to GCF_015476655.1_ASM1547665v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:16,543] [INFO] Task started: fastANI
[2024-01-24 13:41:16,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e3cffdc-4171-4b4c-91c5-dd0184aab6dd/GCF_015476655.1_ASM1547665v1_genomic.fna.gz --refList GCF_015476655.1_ASM1547665v1_genomic.fna/target_genomes.txt --output GCF_015476655.1_ASM1547665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:33,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:33,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg819a530a-7d47-4b5d-bbe4-17969ae6afb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:33,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg819a530a-7d47-4b5d-bbe4-17969ae6afb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:33,883] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:33,883] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:33,884] [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
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	100.0	1935	1938	95	conclusive
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	83.9812	1119	1938	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	77.6197	441	1938	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	77.323	270	1938	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	77.2279	200	1938	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	77.1152	200	1938	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.0708	184	1938	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.01	224	1938	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	76.9489	224	1938	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.7451	183	1938	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	76.5671	80	1938	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.5634	107	1938	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	76.3849	109	1938	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	76.3588	135	1938	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	76.355	115	1938	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.3271	112	1938	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	76.2285	83	1938	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	76.1203	89	1938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,886] [INFO] DFAST Taxonomy check result was written to GCF_015476655.1_ASM1547665v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:33,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:33,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:33,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg819a530a-7d47-4b5d-bbe4-17969ae6afb9/dqc_reference/checkm_data
[2024-01-24 13:41:33,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:33,953] [INFO] Task started: CheckM
[2024-01-24 13:41:33,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015476655.1_ASM1547665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015476655.1_ASM1547665v1_genomic.fna/checkm_input GCF_015476655.1_ASM1547665v1_genomic.fna/checkm_result
[2024-01-24 13:42:56,900] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:56,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:56,922] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:56,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:56,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015476655.1_ASM1547665v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:56,923] [INFO] Task started: Blastn
[2024-01-24 13:42:56,923] [INFO] Running command: blastn -query GCF_015476655.1_ASM1547665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg819a530a-7d47-4b5d-bbe4-17969ae6afb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_015476655.1_ASM1547665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:57,719] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:57,724] [INFO] Selected 19 target genomes.
[2024-01-24 13:42:57,724] [INFO] Target genome list was writen to GCF_015476655.1_ASM1547665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:57,758] [INFO] Task started: fastANI
[2024-01-24 13:42:57,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e3cffdc-4171-4b4c-91c5-dd0184aab6dd/GCF_015476655.1_ASM1547665v1_genomic.fna.gz --refList GCF_015476655.1_ASM1547665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015476655.1_ASM1547665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:14,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:14,284] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:14,284] [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_015476655.1	s__Aquiflexum lacus	100.0	1935	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176595.1	s__Aquiflexum balticum	83.9642	1121	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	79.713	482	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354735.1	s__SW124 sp015354735	79.0612	243	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__SW124	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	77.6793	292	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_003003005.1	s__Mongoliibacter ruber	77.6404	306	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	77.6002	441	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	77.366	296	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	77.3359	268	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	77.2279	200	1938	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	77.1152	200	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	76.9489	224	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.7457	183	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254835.1	s__Algoriphagus aestuariicola	76.5886	80	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	76.3631	109	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571135.1	s__Algoriphagus kandeliae	76.3391	100	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.3271	112	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002002735.1	s__Algoriphagus sp002002735	76.2421	107	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	76.2285	83	1938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:14,286] [INFO] GTDB search result was written to GCF_015476655.1_ASM1547665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:14,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:14,291] [INFO] DFAST_QC result json was written to GCF_015476655.1_ASM1547665v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:14,291] [INFO] DFAST_QC completed!
[2024-01-24 13:43:14,291] [INFO] Total running time: 0h2m30s