[2024-01-24 13:18:27,653] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,655] [INFO] DQC Reference Directory: /var/lib/cwl/stg58509ee1-de7d-4b00-afeb-e07eb30369ed/dqc_reference
[2024-01-24 13:18:28,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:28,962] [INFO] Task started: Prodigal
[2024-01-24 13:18:28,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b998b0b-9a2a-4fa7-ac0b-2adf8968a8b1/GCF_000295935.2_IndiAl02_genomic.fna.gz | prodigal -d GCF_000295935.2_IndiAl02_genomic.fna/cds.fna -a GCF_000295935.2_IndiAl02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:52,208] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:52,209] [INFO] Task started: HMMsearch
[2024-01-24 13:18:52,209] [INFO] Running command: hmmsearch --tblout GCF_000295935.2_IndiAl02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58509ee1-de7d-4b00-afeb-e07eb30369ed/dqc_reference/reference_markers.hmm GCF_000295935.2_IndiAl02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:52,554] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:52,556] [INFO] Found 6/6 markers.
[2024-01-24 13:18:52,599] [INFO] Query marker FASTA was written to GCF_000295935.2_IndiAl02_genomic.fna/markers.fasta
[2024-01-24 13:18:52,599] [INFO] Task started: Blastn
[2024-01-24 13:18:52,600] [INFO] Running command: blastn -query GCF_000295935.2_IndiAl02_genomic.fna/markers.fasta -db /var/lib/cwl/stg58509ee1-de7d-4b00-afeb-e07eb30369ed/dqc_reference/reference_markers.fasta -out GCF_000295935.2_IndiAl02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:53,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:53,251] [INFO] Selected 25 target genomes.
[2024-01-24 13:18:53,251] [INFO] Target genome list was writen to GCF_000295935.2_IndiAl02_genomic.fna/target_genomes.txt
[2024-01-24 13:18:53,261] [INFO] Task started: fastANI
[2024-01-24 13:18:53,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b998b0b-9a2a-4fa7-ac0b-2adf8968a8b1/GCF_000295935.2_IndiAl02_genomic.fna.gz --refList GCF_000295935.2_IndiAl02_genomic.fna/target_genomes.txt --output GCF_000295935.2_IndiAl02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:12,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:12,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58509ee1-de7d-4b00-afeb-e07eb30369ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:12,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58509ee1-de7d-4b00-afeb-e07eb30369ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:13,005] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:13,005] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:13,006] [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
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	79.3523	228	1652	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	78.4254	224	1652	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	78.1258	306	1652	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	78.0781	307	1652	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	77.8404	315	1652	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.7998	205	1652	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	77.5319	203	1652	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	77.4157	191	1652	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	77.3453	296	1652	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	77.1999	203	1652	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.1714	202	1652	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.9343	229	1652	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.661	117	1652	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	76.6469	105	1652	95	below_threshold
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	76.6462	168	1652	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	76.5883	78	1652	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	76.5465	70	1652	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	76.5222	122	1652	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	76.5	101	1652	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.4682	106	1652	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	76.4001	102	1652	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	76.3802	68	1652	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	76.2028	121	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:13,008] [INFO] DFAST Taxonomy check result was written to GCF_000295935.2_IndiAl02_genomic.fna/tc_result.tsv
[2024-01-24 13:19:13,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:13,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:13,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58509ee1-de7d-4b00-afeb-e07eb30369ed/dqc_reference/checkm_data
[2024-01-24 13:19:13,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:13,066] [INFO] Task started: CheckM
[2024-01-24 13:19:13,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000295935.2_IndiAl02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000295935.2_IndiAl02_genomic.fna/checkm_input GCF_000295935.2_IndiAl02_genomic.fna/checkm_result
[2024-01-24 13:20:21,216] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:21,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:21,243] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:21,243] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:21,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000295935.2_IndiAl02_genomic.fna/markers.fasta)
[2024-01-24 13:20:21,244] [INFO] Task started: Blastn
[2024-01-24 13:20:21,244] [INFO] Running command: blastn -query GCF_000295935.2_IndiAl02_genomic.fna/markers.fasta -db /var/lib/cwl/stg58509ee1-de7d-4b00-afeb-e07eb30369ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_000295935.2_IndiAl02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:22,044] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:22,049] [INFO] Selected 19 target genomes.
[2024-01-24 13:20:22,049] [INFO] Target genome list was writen to GCF_000295935.2_IndiAl02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:22,189] [INFO] Task started: fastANI
[2024-01-24 13:20:22,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b998b0b-9a2a-4fa7-ac0b-2adf8968a8b1/GCF_000295935.2_IndiAl02_genomic.fna.gz --refList GCF_000295935.2_IndiAl02_genomic.fna/target_genomes_gtdb.txt --output GCF_000295935.2_IndiAl02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:39,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:39,501] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:39,502] [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_000295935.2	s__Indibacter alkaliphilus	100.0	1649	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000265405.1	s__Belliella baltica	79.3743	227	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	79.1262	641	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	78.8413	607	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	78.1259	306	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	77.8435	314	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	77.6773	226	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_014652135.1	s__Mongoliitalea lutea	77.5469	202	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	77.3454	288	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	77.336	297	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	77.1999	203	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811155.1	s__Lunatimonas salinarum	76.937	65	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655305.1	s__Algoriphagus sp007655305	76.661	117	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429445.1	s__Algoriphagus terrigena	76.6152	77	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119225.1	s__Cyclobacterium sp010119225	76.5465	70	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	76.5125	125	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	76.506	104	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	76.5	101	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	76.2028	121	1652	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 13:20:39,504] [INFO] GTDB search result was written to GCF_000295935.2_IndiAl02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:39,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:39,512] [INFO] DFAST_QC result json was written to GCF_000295935.2_IndiAl02_genomic.fna/dqc_result.json
[2024-01-24 13:20:39,513] [INFO] DFAST_QC completed!
[2024-01-24 13:20:39,513] [INFO] Total running time: 0h2m12s