[2024-01-24 13:32:41,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,110] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,111] [INFO] DQC Reference Directory: /var/lib/cwl/stg1498b070-cca3-437f-a6d7-1c51c9bcb72d/dqc_reference
[2024-01-24 13:32:42,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,387] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg539b74d0-a700-4cb0-9a2e-54031e5ddf6d/GCF_009192725.1_ASM919272v1_genomic.fna.gz | prodigal -d GCF_009192725.1_ASM919272v1_genomic.fna/cds.fna -a GCF_009192725.1_ASM919272v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:52,478] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:52,479] [INFO] Task started: HMMsearch
[2024-01-24 13:32:52,479] [INFO] Running command: hmmsearch --tblout GCF_009192725.1_ASM919272v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1498b070-cca3-437f-a6d7-1c51c9bcb72d/dqc_reference/reference_markers.hmm GCF_009192725.1_ASM919272v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:52,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:52,837] [INFO] Found 6/6 markers.
[2024-01-24 13:32:52,875] [INFO] Query marker FASTA was written to GCF_009192725.1_ASM919272v1_genomic.fna/markers.fasta
[2024-01-24 13:32:52,875] [INFO] Task started: Blastn
[2024-01-24 13:32:52,875] [INFO] Running command: blastn -query GCF_009192725.1_ASM919272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1498b070-cca3-437f-a6d7-1c51c9bcb72d/dqc_reference/reference_markers.fasta -out GCF_009192725.1_ASM919272v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:54,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:54,107] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:54,108] [INFO] Target genome list was writen to GCF_009192725.1_ASM919272v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:54,117] [INFO] Task started: fastANI
[2024-01-24 13:32:54,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg539b74d0-a700-4cb0-9a2e-54031e5ddf6d/GCF_009192725.1_ASM919272v1_genomic.fna.gz --refList GCF_009192725.1_ASM919272v1_genomic.fna/target_genomes.txt --output GCF_009192725.1_ASM919272v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:08,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:08,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1498b070-cca3-437f-a6d7-1c51c9bcb72d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:08,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1498b070-cca3-437f-a6d7-1c51c9bcb72d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:08,585] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:08,585] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:08,585] [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
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.2536	428	1133	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	79.1418	380	1133	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	79.1385	381	1133	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.0522	420	1133	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	78.8532	359	1133	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.8278	313	1133	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.8085	374	1133	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	78.7628	346	1133	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	78.7281	347	1133	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	78.6799	294	1133	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	78.6696	343	1133	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	78.6488	325	1133	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.5994	333	1133	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	78.5788	331	1133	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	78.5573	325	1133	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.4775	333	1133	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	78.4762	361	1133	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	78.4474	344	1133	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.3462	380	1133	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.3389	316	1133	95	below_threshold
Mobilicoccus pelagius	strain=NBRC 104925	GCA_000247995.2	746032	746032	type	True	77.9661	249	1133	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.9316	205	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:08,586] [INFO] DFAST Taxonomy check result was written to GCF_009192725.1_ASM919272v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:08,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:08,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:08,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1498b070-cca3-437f-a6d7-1c51c9bcb72d/dqc_reference/checkm_data
[2024-01-24 13:33:08,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:08,631] [INFO] Task started: CheckM
[2024-01-24 13:33:08,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009192725.1_ASM919272v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009192725.1_ASM919272v1_genomic.fna/checkm_input GCF_009192725.1_ASM919272v1_genomic.fna/checkm_result
[2024-01-24 13:33:46,442] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:46,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:46,459] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:46,459] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:46,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009192725.1_ASM919272v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:46,460] [INFO] Task started: Blastn
[2024-01-24 13:33:46,460] [INFO] Running command: blastn -query GCF_009192725.1_ASM919272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1498b070-cca3-437f-a6d7-1c51c9bcb72d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009192725.1_ASM919272v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:48,627] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:48,630] [INFO] Selected 22 target genomes.
[2024-01-24 13:33:48,630] [INFO] Target genome list was writen to GCF_009192725.1_ASM919272v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:48,641] [INFO] Task started: fastANI
[2024-01-24 13:33:48,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg539b74d0-a700-4cb0-9a2e-54031e5ddf6d/GCF_009192725.1_ASM919272v1_genomic.fna.gz --refList GCF_009192725.1_ASM919272v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009192725.1_ASM919272v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:04,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:04,946] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:04,946] [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_009192725.1	s__Segeticoccus rhizosphaerae	100.0	1119	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Segeticoccus	95.0	99.13	99.13	0.90	0.90	2	conclusive
GCF_006716205.1	s__Oryzihumus leptocrescens	80.1163	459	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428025.1	s__Pedococcus sp001428025	79.4125	406	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	79.3138	427	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_006716095.1	s__Barrientosiimonas humi	79.1809	381	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002846495.1	s__Phycicoccus duodecadis	78.828	362	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715875.1	s__Terrabacter sp006715875	78.8215	397	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001247745.1	s__Luteipulveratus halotolerans	78.8203	373	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717025.1	s__Terrabacter lapilli	78.7621	406	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	95.88	95.88	0.91	0.91	2	-
GCF_000768695.1	s__Knoellia aerolata	78.7538	346	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888335.1	s__Marihabitans sp016888335	78.7369	290	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	78.6805	393	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992835.1	s__Knoellia locipacati	78.6515	353	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408565.1	s__Janibacter alkaliphilus	78.6475	324	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014518425.1	s__Terrabacter sp014518425	78.5106	389	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635045.1	s__Terracoccus luteus	78.4949	398	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	98.59	98.59	0.96	0.96	2	-
GCF_000576595.1	s__Humihabitans oryzae	78.4901	366	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	78.4681	361	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.3783	377	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCA_012927555.1	s__UBA4719 sp012927555	78.2896	282	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	99.32	99.32	0.85	0.85	2	-
GCA_003132125.1	s__UBA4719 sp003132125	77.9584	250	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014857905.1	s__JACYXE01 sp014857905	77.8685	309	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:04,947] [INFO] GTDB search result was written to GCF_009192725.1_ASM919272v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:04,948] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:04,951] [INFO] DFAST_QC result json was written to GCF_009192725.1_ASM919272v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:04,951] [INFO] DFAST_QC completed!
[2024-01-24 13:34:04,951] [INFO] Total running time: 0h1m24s