[2023-06-27 05:00:35,900] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:00:35,903] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:00:35,903] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6a8dd4e-a1af-4d7f-9bee-17e41980832b/dqc_reference
[2023-06-27 05:00:37,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:00:37,167] [INFO] Task started: Prodigal
[2023-06-27 05:00:37,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e503540-9574-4841-8e2f-b3936c6ffda3/GCA_002428565.1_ASM242856v1_genomic.fna.gz | prodigal -d GCA_002428565.1_ASM242856v1_genomic.fna/cds.fna -a GCA_002428565.1_ASM242856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:00:49,934] [INFO] Task succeeded: Prodigal
[2023-06-27 05:00:49,934] [INFO] Task started: HMMsearch
[2023-06-27 05:00:49,934] [INFO] Running command: hmmsearch --tblout GCA_002428565.1_ASM242856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6a8dd4e-a1af-4d7f-9bee-17e41980832b/dqc_reference/reference_markers.hmm GCA_002428565.1_ASM242856v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:00:50,233] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:00:50,234] [INFO] Found 6/6 markers.
[2023-06-27 05:00:50,281] [INFO] Query marker FASTA was written to GCA_002428565.1_ASM242856v1_genomic.fna/markers.fasta
[2023-06-27 05:00:50,282] [INFO] Task started: Blastn
[2023-06-27 05:00:50,282] [INFO] Running command: blastn -query GCA_002428565.1_ASM242856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6a8dd4e-a1af-4d7f-9bee-17e41980832b/dqc_reference/reference_markers.fasta -out GCA_002428565.1_ASM242856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:00:50,891] [INFO] Task succeeded: Blastn
[2023-06-27 05:00:50,894] [INFO] Selected 23 target genomes.
[2023-06-27 05:00:50,895] [INFO] Target genome list was writen to GCA_002428565.1_ASM242856v1_genomic.fna/target_genomes.txt
[2023-06-27 05:00:50,903] [INFO] Task started: fastANI
[2023-06-27 05:00:50,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e503540-9574-4841-8e2f-b3936c6ffda3/GCA_002428565.1_ASM242856v1_genomic.fna.gz --refList GCA_002428565.1_ASM242856v1_genomic.fna/target_genomes.txt --output GCA_002428565.1_ASM242856v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:01:05,843] [INFO] Task succeeded: fastANI
[2023-06-27 05:01:05,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6a8dd4e-a1af-4d7f-9bee-17e41980832b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:01:05,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6a8dd4e-a1af-4d7f-9bee-17e41980832b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:01:05,857] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:01:05,857] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:01:05,857] [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
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	76.3596	129	1343	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	76.3183	127	1343	95	below_threshold
Longilinea arvoryzae	strain=KOME-1	GCA_001050235.2	360412	360412	type	True	76.0676	101	1343	95	below_threshold
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	76.0229	65	1343	95	below_threshold
Anaerolinea thermophila	strain=UNI-1	GCA_000199675.1	167964	167964	type	True	75.9977	60	1343	95	below_threshold
Aggregatilinea lenta	strain=MO-CFX2	GCA_003569045.1	913108	913108	type	True	75.3314	61	1343	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:01:05,859] [INFO] DFAST Taxonomy check result was written to GCA_002428565.1_ASM242856v1_genomic.fna/tc_result.tsv
[2023-06-27 05:01:05,860] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:01:05,860] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:01:05,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6a8dd4e-a1af-4d7f-9bee-17e41980832b/dqc_reference/checkm_data
[2023-06-27 05:01:05,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:01:05,907] [INFO] Task started: CheckM
[2023-06-27 05:01:05,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002428565.1_ASM242856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002428565.1_ASM242856v1_genomic.fna/checkm_input GCA_002428565.1_ASM242856v1_genomic.fna/checkm_result
[2023-06-27 05:01:45,583] [INFO] Task succeeded: CheckM
[2023-06-27 05:01:45,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:01:45,610] [INFO] ===== Completeness check finished =====
[2023-06-27 05:01:45,611] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:01:45,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002428565.1_ASM242856v1_genomic.fna/markers.fasta)
[2023-06-27 05:01:45,611] [INFO] Task started: Blastn
[2023-06-27 05:01:45,612] [INFO] Running command: blastn -query GCA_002428565.1_ASM242856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6a8dd4e-a1af-4d7f-9bee-17e41980832b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002428565.1_ASM242856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:01:46,480] [INFO] Task succeeded: Blastn
[2023-06-27 05:01:46,486] [INFO] Selected 29 target genomes.
[2023-06-27 05:01:46,486] [INFO] Target genome list was writen to GCA_002428565.1_ASM242856v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:01:46,513] [INFO] Task started: fastANI
[2023-06-27 05:01:46,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e503540-9574-4841-8e2f-b3936c6ffda3/GCA_002428565.1_ASM242856v1_genomic.fna.gz --refList GCA_002428565.1_ASM242856v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002428565.1_ASM242856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:02:02,586] [INFO] Task succeeded: fastANI
[2023-06-27 05:02:02,608] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:02:02,608] [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
GCA_002428565.1	s__UBA6092 sp002428565	100.0	1337	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016932955.1	s__UBA6092 sp016932955	77.5329	282	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772985.1	s__UBA877 sp009772985	76.4645	142	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516075.1	s__JAAYXE01 sp012516075	76.4559	107	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__JAAYXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935755.1	s__JAFGQI01 sp016935755	76.3984	120	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__JAFGQI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306035.1	s__Levilinea saccharolytica	76.3329	131	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea	95.0	99.90	99.90	0.95	0.95	2	-
GCA_011329365.1	s__DSTM01 sp011329365	76.3057	111	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__DSTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872065.1	s__CAIQJJ01 sp903872065	76.2304	122	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__CAIQJJ01	95.0	99.39	99.39	0.86	0.86	2	-
GCA_016934715.1	s__JAFGSI01 sp016934715	76.2281	115	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__JAFGSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385985.1	s__UBA3924 sp002385985	76.2035	114	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924	95.0	99.86	99.86	0.92	0.92	2	-
GCA_016191875.1	s__SCUK01 sp016191875	76.1788	123	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__SCUK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903829085.1	s__UBA877 sp903829085	76.1544	60	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055765.1	s__DSOS01 sp011055765	76.1092	106	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__DSOS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795165.1	s__RBG-16-57-11 sp001795165	76.0351	106	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__RBG-16-57-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051635.1	s__DRKV01 sp011051635	76.0235	84	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRKV01;g__DRKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000199675.1	s__Anaerolinea thermophila	75.9977	60	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055775.1	s__DSPF01 sp011055775	75.9754	62	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__DSPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789165.1	s__SpSt-583 sp016789165	75.949	102	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011176535.1	s__DUEP01 sp011176535	75.831	61	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRMV01;g__DUEP01	95.0	99.79	99.71	0.93	0.89	3	-
GCA_016935415.1	s__JAFGRA01 sp016935415	75.7563	81	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__JAFGRA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250455.1	s__UBA11579 sp003250455	75.7176	65	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__UBA11579	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860725.1	s__CTSoil-045 sp017860725	75.6693	54	1343	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__CTSoil-045	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:02:02,611] [INFO] GTDB search result was written to GCA_002428565.1_ASM242856v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:02:02,611] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:02:02,622] [INFO] DFAST_QC result json was written to GCA_002428565.1_ASM242856v1_genomic.fna/dqc_result.json
[2023-06-27 05:02:02,622] [INFO] DFAST_QC completed!
[2023-06-27 05:02:02,622] [INFO] Total running time: 0h1m27s