[2024-01-25 19:10:35,774] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:35,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:35,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb13e716-11b2-4f93-8ae8-c75cd0bd3538/dqc_reference
[2024-01-25 19:10:36,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:36,956] [INFO] Task started: Prodigal
[2024-01-25 19:10:36,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg33715096-95ec-483f-ab49-3e2f1733e590/GCF_028532485.1_ASM2853248v1_genomic.fna.gz | prodigal -d GCF_028532485.1_ASM2853248v1_genomic.fna/cds.fna -a GCF_028532485.1_ASM2853248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:48,392] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:48,392] [INFO] Task started: HMMsearch
[2024-01-25 19:10:48,393] [INFO] Running command: hmmsearch --tblout GCF_028532485.1_ASM2853248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb13e716-11b2-4f93-8ae8-c75cd0bd3538/dqc_reference/reference_markers.hmm GCF_028532485.1_ASM2853248v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:48,633] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:48,634] [INFO] Found 6/6 markers.
[2024-01-25 19:10:48,674] [INFO] Query marker FASTA was written to GCF_028532485.1_ASM2853248v1_genomic.fna/markers.fasta
[2024-01-25 19:10:48,674] [INFO] Task started: Blastn
[2024-01-25 19:10:48,674] [INFO] Running command: blastn -query GCF_028532485.1_ASM2853248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb13e716-11b2-4f93-8ae8-c75cd0bd3538/dqc_reference/reference_markers.fasta -out GCF_028532485.1_ASM2853248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:49,498] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:49,501] [INFO] Selected 20 target genomes.
[2024-01-25 19:10:49,501] [INFO] Target genome list was writen to GCF_028532485.1_ASM2853248v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:49,520] [INFO] Task started: fastANI
[2024-01-25 19:10:49,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg33715096-95ec-483f-ab49-3e2f1733e590/GCF_028532485.1_ASM2853248v1_genomic.fna.gz --refList GCF_028532485.1_ASM2853248v1_genomic.fna/target_genomes.txt --output GCF_028532485.1_ASM2853248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:06,094] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:06,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb13e716-11b2-4f93-8ae8-c75cd0bd3538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:06,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb13e716-11b2-4f93-8ae8-c75cd0bd3538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:06,106] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:11:06,106] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:11:06,107] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.6517	511	1525	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.6297	535	1525	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.1488	342	1525	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.2267	421	1525	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.2179	303	1525	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.8984	233	1525	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_001997295.1	1610493	1610493	type	True	75.5939	117	1525	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_900107385.1	1610493	1610493	type	True	75.552	118	1525	95	below_threshold
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	75.5325	144	1525	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	75.3731	329	1525	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	75.2969	352	1525	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	75.2894	431	1525	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	75.2513	436	1525	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	75.2155	408	1525	95	below_threshold
Kribbella sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	75.2109	248	1525	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	75.1916	475	1525	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	75.1708	249	1525	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	75.1624	340	1525	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	74.9857	77	1525	95	below_threshold
Zobellella taiwanensis	strain=JCM 13381	GCA_003012795.1	347535	347535	type	True	74.8008	76	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:06,109] [INFO] DFAST Taxonomy check result was written to GCF_028532485.1_ASM2853248v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:06,109] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:06,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:06,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb13e716-11b2-4f93-8ae8-c75cd0bd3538/dqc_reference/checkm_data
[2024-01-25 19:11:06,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:06,161] [INFO] Task started: CheckM
[2024-01-25 19:11:06,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028532485.1_ASM2853248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028532485.1_ASM2853248v1_genomic.fna/checkm_input GCF_028532485.1_ASM2853248v1_genomic.fna/checkm_result
[2024-01-25 19:13:08,379] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:08,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:08,413] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:08,414] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:08,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028532485.1_ASM2853248v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:08,415] [INFO] Task started: Blastn
[2024-01-25 19:13:08,415] [INFO] Running command: blastn -query GCF_028532485.1_ASM2853248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb13e716-11b2-4f93-8ae8-c75cd0bd3538/dqc_reference/reference_markers_gtdb.fasta -out GCF_028532485.1_ASM2853248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:09,796] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:09,800] [INFO] Selected 17 target genomes.
[2024-01-25 19:13:09,800] [INFO] Target genome list was writen to GCF_028532485.1_ASM2853248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:09,818] [INFO] Task started: fastANI
[2024-01-25 19:13:09,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg33715096-95ec-483f-ab49-3e2f1733e590/GCF_028532485.1_ASM2853248v1_genomic.fna.gz --refList GCF_028532485.1_ASM2853248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028532485.1_ASM2853248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:22,970] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:22,981] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:13:22,982] [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_012730075.1	s__JAAYBP01 sp012730075	80.4093	545	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	78.7368	768	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513855.1	s__JAAZBK01 sp012513855	78.1161	391	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	78.0819	460	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702505.1	s__JAAZBK01 sp016702505	77.8919	341	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.7426	532	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	77.6666	508	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247975.1	s__JAFBAD01 sp019247975	77.6594	333	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAFBAD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	77.5698	419	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	77.4527	627	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121465.1	s__SKKL01 sp007121465	77.3971	322	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	77.387	482	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781105.1	s__JADDRA01 sp016781105	77.3245	360	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__JADDRA01	95.0	99.25	99.25	0.80	0.80	2	-
GCA_902805555.1	s__CADCSY01 sp902805555	77.0856	368	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002861595.1	s__GCA-2861595 sp002861595	77.069	256	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__GCA-2861595;g__GCA-2861595	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962875.1	s__AWTP1-35 sp003962875	76.8999	338	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873135.1	s__SXMI01 sp903873135	76.6707	324	1525	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:22,985] [INFO] GTDB search result was written to GCF_028532485.1_ASM2853248v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:22,986] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:22,989] [INFO] DFAST_QC result json was written to GCF_028532485.1_ASM2853248v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:22,989] [INFO] DFAST_QC completed!
[2024-01-25 19:13:22,989] [INFO] Total running time: 0h2m47s