[2023-06-26 22:37:33,186] [INFO] DFAST_QC pipeline started.
[2023-06-26 22:37:33,188] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 22:37:33,189] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1a87917-ce9c-4614-83ae-31f83c45d75a/dqc_reference
[2023-06-26 22:37:34,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 22:37:34,503] [INFO] Task started: Prodigal
[2023-06-26 22:37:34,503] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcacf663-ab9a-45f9-b14c-9a9b562dd026/GCA_026647335.1_ASM2664733v1_genomic.fna.gz | prodigal -d GCA_026647335.1_ASM2664733v1_genomic.fna/cds.fna -a GCA_026647335.1_ASM2664733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 22:37:42,194] [INFO] Task succeeded: Prodigal
[2023-06-26 22:37:42,194] [INFO] Task started: HMMsearch
[2023-06-26 22:37:42,194] [INFO] Running command: hmmsearch --tblout GCA_026647335.1_ASM2664733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1a87917-ce9c-4614-83ae-31f83c45d75a/dqc_reference/reference_markers.hmm GCA_026647335.1_ASM2664733v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 22:37:42,469] [INFO] Task succeeded: HMMsearch
[2023-06-26 22:37:42,473] [INFO] Found 6/6 markers.
[2023-06-26 22:37:42,510] [INFO] Query marker FASTA was written to GCA_026647335.1_ASM2664733v1_genomic.fna/markers.fasta
[2023-06-26 22:37:42,511] [INFO] Task started: Blastn
[2023-06-26 22:37:42,511] [INFO] Running command: blastn -query GCA_026647335.1_ASM2664733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1a87917-ce9c-4614-83ae-31f83c45d75a/dqc_reference/reference_markers.fasta -out GCA_026647335.1_ASM2664733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:37:43,166] [INFO] Task succeeded: Blastn
[2023-06-26 22:37:43,176] [INFO] Selected 24 target genomes.
[2023-06-26 22:37:43,176] [INFO] Target genome list was writen to GCA_026647335.1_ASM2664733v1_genomic.fna/target_genomes.txt
[2023-06-26 22:37:43,181] [INFO] Task started: fastANI
[2023-06-26 22:37:43,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcacf663-ab9a-45f9-b14c-9a9b562dd026/GCA_026647335.1_ASM2664733v1_genomic.fna.gz --refList GCA_026647335.1_ASM2664733v1_genomic.fna/target_genomes.txt --output GCA_026647335.1_ASM2664733v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 22:38:02,021] [INFO] Task succeeded: fastANI
[2023-06-26 22:38:02,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1a87917-ce9c-4614-83ae-31f83c45d75a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 22:38:02,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1a87917-ce9c-4614-83ae-31f83c45d75a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 22:38:02,045] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 22:38:02,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 22:38:02,045] [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
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.0998	85	941	95	below_threshold
Arthrobacter pityocampae	strain=Tp2	GCA_002927275.1	547334	547334	type	True	74.9999	64	941	95	below_threshold
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	74.9662	60	941	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9639	171	941	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	74.9577	90	941	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	74.9254	91	941	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	74.9101	119	941	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.9093	222	941	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	74.8894	106	941	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8537	187	941	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.8521	146	941	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	74.8368	128	941	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	74.8121	87	941	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	74.7599	131	941	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.722	175	941	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	74.6435	51	941	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	74.6389	60	941	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	74.6286	56	941	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 22:38:02,055] [INFO] DFAST Taxonomy check result was written to GCA_026647335.1_ASM2664733v1_genomic.fna/tc_result.tsv
[2023-06-26 22:38:02,056] [INFO] ===== Taxonomy check completed =====
[2023-06-26 22:38:02,056] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 22:38:02,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1a87917-ce9c-4614-83ae-31f83c45d75a/dqc_reference/checkm_data
[2023-06-26 22:38:02,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 22:38:02,123] [INFO] Task started: CheckM
[2023-06-26 22:38:02,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026647335.1_ASM2664733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026647335.1_ASM2664733v1_genomic.fna/checkm_input GCA_026647335.1_ASM2664733v1_genomic.fna/checkm_result
[2023-06-26 22:38:31,024] [INFO] Task succeeded: CheckM
[2023-06-26 22:38:31,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.56%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 22:38:31,052] [INFO] ===== Completeness check finished =====
[2023-06-26 22:38:31,053] [INFO] ===== Start GTDB Search =====
[2023-06-26 22:38:31,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026647335.1_ASM2664733v1_genomic.fna/markers.fasta)
[2023-06-26 22:38:31,054] [INFO] Task started: Blastn
[2023-06-26 22:38:31,054] [INFO] Running command: blastn -query GCA_026647335.1_ASM2664733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1a87917-ce9c-4614-83ae-31f83c45d75a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026647335.1_ASM2664733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:38:32,042] [INFO] Task succeeded: Blastn
[2023-06-26 22:38:32,047] [INFO] Selected 30 target genomes.
[2023-06-26 22:38:32,047] [INFO] Target genome list was writen to GCA_026647335.1_ASM2664733v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 22:38:32,068] [INFO] Task started: fastANI
[2023-06-26 22:38:32,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcacf663-ab9a-45f9-b14c-9a9b562dd026/GCA_026647335.1_ASM2664733v1_genomic.fna.gz --refList GCA_026647335.1_ASM2664733v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026647335.1_ASM2664733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 22:38:57,963] [INFO] Task succeeded: fastANI
[2023-06-26 22:38:57,980] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 22:38:57,981] [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_016192525.1	s__JACPTZ01 sp016192525	75.5101	65	941	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPTZ01;g__JACPTZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525755.1	s__PLA2 sp011525755	75.234	168	941	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__PLA2;g__PLA2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903914415.1	s__Fen-1342 sp903914415	75.1806	60	941	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__Fen-1342	95.0	99.57	99.48	0.90	0.90	3	-
GCA_016220045.1	s__JACRIP01 sp016220045	75.0925	140	941	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPWG01;g__JACRIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011065895.1	s__Paludisphaera sp011065895	75.0736	89	941	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200125.1	s__JACQFK01 sp016200125	74.9997	91	941	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__MHYJ01;f__JACPRB01;g__JACQFK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	74.9632	191	941	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	74.9613	172	941	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979235.1	s__Dissulfurirhabdus thermomarina	74.8986	123	941	d__Bacteria;p__Desulfobacterota;c__Dissulfuribacteria;o__Dissulfuribacterales;f__Dissulfurirhabdaceae;g__Dissulfurirhabdus	95.0	99.96	99.96	0.96	0.96	2	-
GCF_011064615.1	s__Aquisphaera sp011064615	74.8908	145	941	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610895.1	s__Paludisphaera sp001610895	74.8883	135	941	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	74.8792	159	941	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
GCF_002994615.1	s__Enhygromyxa salina_A	74.8698	125	941	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602285.1	s__Arthrobacter_D sp003602285	74.8004	58	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	95.90	95.90	0.84	0.84	2	-
GCA_017527155.1	s__CACXEY01 sp017527155	74.7918	108	941	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__CACXEY01	95.0	97.65	97.65	0.79	0.79	2	-
GCA_016930695.1	s__JAFGGD01 sp016930695	74.7853	58	941	d__Bacteria;p__JABDJQ01;c__JABDJQ01;o__JABDJQ01;f__JABDJQ01;g__JAFGGD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737335.2	s__Enhygromyxa salina_C	74.7796	71	941	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405885.1	s__Arthrobacter_D sp016405885	74.7679	50	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928275.1	s__CAIYQJ01 sp903928275	74.7529	77	941	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIYQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921205.1	s__Actinophytocola xanthii	74.7475	136	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014730065.1	s__UBA1398 sp014730065	74.6567	50	941	d__Bacteria;p__Armatimonadota;c__UBA5377;o__UBA1398;f__UBA1398;g__UBA1398	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	74.6082	95	941	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 22:38:57,983] [INFO] GTDB search result was written to GCA_026647335.1_ASM2664733v1_genomic.fna/result_gtdb.tsv
[2023-06-26 22:38:57,984] [INFO] ===== GTDB Search completed =====
[2023-06-26 22:38:57,989] [INFO] DFAST_QC result json was written to GCA_026647335.1_ASM2664733v1_genomic.fna/dqc_result.json
[2023-06-26 22:38:57,990] [INFO] DFAST_QC completed!
[2023-06-26 22:38:57,990] [INFO] Total running time: 0h1m25s