[2024-01-24 13:28:28,992] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,994] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc04e8f2-1d68-4e5d-aea5-ad73e1738fa4/dqc_reference
[2024-01-24 13:28:30,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,277] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,277] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6f117ac-84d8-43ad-937a-fbd539f0c9e1/GCF_008580665.1_NCCP-1664_genomic.fna.gz | prodigal -d GCF_008580665.1_NCCP-1664_genomic.fna/cds.fna -a GCF_008580665.1_NCCP-1664_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:39,924] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:39,925] [INFO] Task started: HMMsearch
[2024-01-24 13:28:39,925] [INFO] Running command: hmmsearch --tblout GCF_008580665.1_NCCP-1664_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc04e8f2-1d68-4e5d-aea5-ad73e1738fa4/dqc_reference/reference_markers.hmm GCF_008580665.1_NCCP-1664_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:40,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:40,204] [INFO] Found 6/6 markers.
[2024-01-24 13:28:40,234] [INFO] Query marker FASTA was written to GCF_008580665.1_NCCP-1664_genomic.fna/markers.fasta
[2024-01-24 13:28:40,234] [INFO] Task started: Blastn
[2024-01-24 13:28:40,234] [INFO] Running command: blastn -query GCF_008580665.1_NCCP-1664_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc04e8f2-1d68-4e5d-aea5-ad73e1738fa4/dqc_reference/reference_markers.fasta -out GCF_008580665.1_NCCP-1664_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:41,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:41,432] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:41,433] [INFO] Target genome list was writen to GCF_008580665.1_NCCP-1664_genomic.fna/target_genomes.txt
[2024-01-24 13:28:41,445] [INFO] Task started: fastANI
[2024-01-24 13:28:41,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6f117ac-84d8-43ad-937a-fbd539f0c9e1/GCF_008580665.1_NCCP-1664_genomic.fna.gz --refList GCF_008580665.1_NCCP-1664_genomic.fna/target_genomes.txt --output GCF_008580665.1_NCCP-1664_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:55,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:55,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc04e8f2-1d68-4e5d-aea5-ad73e1738fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:55,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc04e8f2-1d68-4e5d-aea5-ad73e1738fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:55,246] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:55,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:55,246] [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
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	80.0201	500	1074	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	79.944	482	1074	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	79.8044	427	1074	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	79.6122	430	1074	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	79.5959	446	1074	95	below_threshold
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	79.3631	348	1074	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	79.1937	389	1074	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.8851	354	1074	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	78.8725	353	1074	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	78.8473	314	1074	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.8434	358	1074	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	78.8132	341	1074	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	78.7986	307	1074	95	below_threshold
Citricoccus muralis	strain=DSM 14442	GCA_003386075.1	169134	169134	type	True	78.7725	307	1074	95	below_threshold
Tersicoccus solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	78.7204	326	1074	95	below_threshold
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	78.7095	310	1074	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	78.6665	329	1074	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	78.5861	327	1074	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.4683	318	1074	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	78.3192	285	1074	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:55,248] [INFO] DFAST Taxonomy check result was written to GCF_008580665.1_NCCP-1664_genomic.fna/tc_result.tsv
[2024-01-24 13:28:55,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:55,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:55,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc04e8f2-1d68-4e5d-aea5-ad73e1738fa4/dqc_reference/checkm_data
[2024-01-24 13:28:55,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:55,282] [INFO] Task started: CheckM
[2024-01-24 13:28:55,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008580665.1_NCCP-1664_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008580665.1_NCCP-1664_genomic.fna/checkm_input GCF_008580665.1_NCCP-1664_genomic.fna/checkm_result
[2024-01-24 13:29:26,804] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:26,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:26,833] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:26,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:26,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008580665.1_NCCP-1664_genomic.fna/markers.fasta)
[2024-01-24 13:29:26,834] [INFO] Task started: Blastn
[2024-01-24 13:29:26,834] [INFO] Running command: blastn -query GCF_008580665.1_NCCP-1664_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc04e8f2-1d68-4e5d-aea5-ad73e1738fa4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008580665.1_NCCP-1664_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:28,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:28,832] [INFO] Selected 14 target genomes.
[2024-01-24 13:29:28,832] [INFO] Target genome list was writen to GCF_008580665.1_NCCP-1664_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:28,847] [INFO] Task started: fastANI
[2024-01-24 13:29:28,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6f117ac-84d8-43ad-937a-fbd539f0c9e1/GCF_008580665.1_NCCP-1664_genomic.fna.gz --refList GCF_008580665.1_NCCP-1664_genomic.fna/target_genomes_gtdb.txt --output GCF_008580665.1_NCCP-1664_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:39,595] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:39,607] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:39,607] [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_008580665.1	s__Zafaria cholistanensis	100.0	1072	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019084045.1	s__Paeniglutamicibacter sp019084045	80.1993	467	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001863355.1	s__Paeniglutamicibacter sp001863355	80.0509	481	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395835.1	s__Arthrobacter_F mobilis	80.01	501	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876575.1	s__Paeniglutamicibacter psychrophenolicus	79.9389	482	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287975.1	s__Paeniglutamicibacter sp003287975	79.894	479	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	79.8532	409	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	79.8309	424	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651715.1	s__Zhihengliuella salsuginis	79.6205	429	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328305.2	s__Arthrobacter_F crystallopoietes_A	79.3979	366	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224415.1	s__Citricoccus sp000224415	79.2286	375	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	96.24	96.24	0.87	0.87	2	-
GCF_005877055.1	s__Citricoccus sp005877055	79.1159	403	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386075.1	s__Citricoccus muralis	78.8137	304	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193255.1	s__Arthrobacter_B koreensis	78.5861	327	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:39,609] [INFO] GTDB search result was written to GCF_008580665.1_NCCP-1664_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:39,609] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:39,614] [INFO] DFAST_QC result json was written to GCF_008580665.1_NCCP-1664_genomic.fna/dqc_result.json
[2024-01-24 13:29:39,614] [INFO] DFAST_QC completed!
[2024-01-24 13:29:39,614] [INFO] Total running time: 0h1m11s