[2024-01-24 13:49:29,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,147] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6da20b2-f436-4ca8-82ea-659799a38bd5/dqc_reference
[2024-01-24 13:49:30,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:30,479] [INFO] Task started: Prodigal
[2024-01-24 13:49:30,479] [INFO] Running command: gunzip -c /var/lib/cwl/stga0b2f320-4d21-471b-940b-143a07162d24/GCF_009371985.2_ASM937198v2_genomic.fna.gz | prodigal -d GCF_009371985.2_ASM937198v2_genomic.fna/cds.fna -a GCF_009371985.2_ASM937198v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:55,681] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:55,682] [INFO] Task started: HMMsearch
[2024-01-24 13:49:55,682] [INFO] Running command: hmmsearch --tblout GCF_009371985.2_ASM937198v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6da20b2-f436-4ca8-82ea-659799a38bd5/dqc_reference/reference_markers.hmm GCF_009371985.2_ASM937198v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:56,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:56,098] [INFO] Found 6/6 markers.
[2024-01-24 13:49:56,161] [INFO] Query marker FASTA was written to GCF_009371985.2_ASM937198v2_genomic.fna/markers.fasta
[2024-01-24 13:49:56,161] [INFO] Task started: Blastn
[2024-01-24 13:49:56,162] [INFO] Running command: blastn -query GCF_009371985.2_ASM937198v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6da20b2-f436-4ca8-82ea-659799a38bd5/dqc_reference/reference_markers.fasta -out GCF_009371985.2_ASM937198v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:56,840] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:56,844] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:56,845] [INFO] Target genome list was writen to GCF_009371985.2_ASM937198v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:56,854] [INFO] Task started: fastANI
[2024-01-24 13:49:56,854] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b2f320-4d21-471b-940b-143a07162d24/GCF_009371985.2_ASM937198v2_genomic.fna.gz --refList GCF_009371985.2_ASM937198v2_genomic.fna/target_genomes.txt --output GCF_009371985.2_ASM937198v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:09,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:09,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6da20b2-f436-4ca8-82ea-659799a38bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:09,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6da20b2-f436-4ca8-82ea-659799a38bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:09,651] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:09,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:09,651] [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
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	100.0	1507	1510	95	conclusive
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.9906	199	1510	95	below_threshold
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	76.6599	119	1510	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.5911	117	1510	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	76.562	112	1510	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	76.5494	110	1510	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.5401	87	1510	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	76.4391	81	1510	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.3231	145	1510	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.3217	145	1510	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	76.2271	149	1510	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.1025	106	1510	95	below_threshold
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	75.9999	52	1510	95	below_threshold
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	75.9607	64	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:09,653] [INFO] DFAST Taxonomy check result was written to GCF_009371985.2_ASM937198v2_genomic.fna/tc_result.tsv
[2024-01-24 13:50:09,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:09,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:09,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6da20b2-f436-4ca8-82ea-659799a38bd5/dqc_reference/checkm_data
[2024-01-24 13:50:09,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:09,705] [INFO] Task started: CheckM
[2024-01-24 13:50:09,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009371985.2_ASM937198v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009371985.2_ASM937198v2_genomic.fna/checkm_input GCF_009371985.2_ASM937198v2_genomic.fna/checkm_result
[2024-01-24 13:51:17,657] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:17,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:17,679] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:17,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:17,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009371985.2_ASM937198v2_genomic.fna/markers.fasta)
[2024-01-24 13:51:17,681] [INFO] Task started: Blastn
[2024-01-24 13:51:17,681] [INFO] Running command: blastn -query GCF_009371985.2_ASM937198v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6da20b2-f436-4ca8-82ea-659799a38bd5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009371985.2_ASM937198v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:18,457] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:18,461] [INFO] Selected 22 target genomes.
[2024-01-24 13:51:18,462] [INFO] Target genome list was writen to GCF_009371985.2_ASM937198v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:18,502] [INFO] Task started: fastANI
[2024-01-24 13:51:18,502] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b2f320-4d21-471b-940b-143a07162d24/GCF_009371985.2_ASM937198v2_genomic.fna.gz --refList GCF_009371985.2_ASM937198v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009371985.2_ASM937198v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:32,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:32,962] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:32,963] [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_009371985.2	s__TP-CH-4 sp009371985	100.0	1507	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TP-CH-4	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005943945.1	s__F202Z8 sp005943945	77.0037	197	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__F202Z8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008367235.1	s__Pareuzebyella sediminis	76.6599	119	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pareuzebyella	95.0	99.39	99.39	0.97	0.97	2	-
GCF_009674825.1	s__Maribacter_A luteus	76.5911	117	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885635.1	s__RZ26 sp005885635	76.5728	134	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	76.5634	86	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.528	135	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638095.1	s__Muriicola marianensis	76.4279	71	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103215.1	s__Kriegella aquimaris	76.3919	120	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kriegella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002749285.1	s__Maribacter_A sp002749285	76.3488	63	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.3217	145	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_013402795.1	s__Costertonia aggregata	76.223	148	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	76.1495	114	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	76.0968	88	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177645.1	s__Arenibacter troitsensis	76.0875	104	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426735.1	s__Arenibacter sp003426735	76.0441	111	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024125.1	s__Robiginitalea biformata	75.9999	52	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198115.1	s__Robiginitalea sediminis	75.9607	64	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	75.8703	117	1510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:32,964] [INFO] GTDB search result was written to GCF_009371985.2_ASM937198v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:32,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:32,968] [INFO] DFAST_QC result json was written to GCF_009371985.2_ASM937198v2_genomic.fna/dqc_result.json
[2024-01-24 13:51:32,969] [INFO] DFAST_QC completed!
[2024-01-24 13:51:32,969] [INFO] Total running time: 0h2m4s