[2024-01-24 13:40:32,625] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:32,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:32,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg153d75c5-b906-49a1-ad68-4aec91c18425/dqc_reference
[2024-01-24 13:40:33,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:33,940] [INFO] Task started: Prodigal
[2024-01-24 13:40:33,940] [INFO] Running command: gunzip -c /var/lib/cwl/stga040d5d3-c630-44d2-a727-647d7968101e/GCF_021398215.1_ASM2139821v1_genomic.fna.gz | prodigal -d GCF_021398215.1_ASM2139821v1_genomic.fna/cds.fna -a GCF_021398215.1_ASM2139821v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,110] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,110] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,110] [INFO] Running command: hmmsearch --tblout GCF_021398215.1_ASM2139821v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153d75c5-b906-49a1-ad68-4aec91c18425/dqc_reference/reference_markers.hmm GCF_021398215.1_ASM2139821v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:48,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:48,437] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,477] [INFO] Query marker FASTA was written to GCF_021398215.1_ASM2139821v1_genomic.fna/markers.fasta
[2024-01-24 13:40:48,477] [INFO] Task started: Blastn
[2024-01-24 13:40:48,477] [INFO] Running command: blastn -query GCF_021398215.1_ASM2139821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153d75c5-b906-49a1-ad68-4aec91c18425/dqc_reference/reference_markers.fasta -out GCF_021398215.1_ASM2139821v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:49,376] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:49,380] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:49,380] [INFO] Target genome list was writen to GCF_021398215.1_ASM2139821v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:49,387] [INFO] Task started: fastANI
[2024-01-24 13:40:49,388] [INFO] Running command: fastANI --query /var/lib/cwl/stga040d5d3-c630-44d2-a727-647d7968101e/GCF_021398215.1_ASM2139821v1_genomic.fna.gz --refList GCF_021398215.1_ASM2139821v1_genomic.fna/target_genomes.txt --output GCF_021398215.1_ASM2139821v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:57,918] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:57,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153d75c5-b906-49a1-ad68-4aec91c18425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:57,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153d75c5-b906-49a1-ad68-4aec91c18425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:57,929] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:40:57,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:40:57,929] [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 psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	81.1714	648	1390	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=GP3	GCA_003185915.1	291045	291045	type	True	81.0176	628	1390	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	80.2313	592	1390	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	80.1965	585	1390	95	below_threshold
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	80.093	552	1390	95	below_threshold
Arthrobacter psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	79.9659	465	1390	95	below_threshold
Arthrobacter cryoconiti	strain=Cr6-08	GCA_020905375.1	748907	748907	type	True	78.8905	295	1390	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	78.838	445	1390	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.622	158	1390	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	78.3632	189	1390	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	76.7104	151	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:57,931] [INFO] DFAST Taxonomy check result was written to GCF_021398215.1_ASM2139821v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:57,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:57,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:57,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153d75c5-b906-49a1-ad68-4aec91c18425/dqc_reference/checkm_data
[2024-01-24 13:40:57,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:57,974] [INFO] Task started: CheckM
[2024-01-24 13:40:57,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021398215.1_ASM2139821v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021398215.1_ASM2139821v1_genomic.fna/checkm_input GCF_021398215.1_ASM2139821v1_genomic.fna/checkm_result
[2024-01-24 13:41:42,676] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:42,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:42,708] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:42,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:42,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021398215.1_ASM2139821v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:42,709] [INFO] Task started: Blastn
[2024-01-24 13:41:42,709] [INFO] Running command: blastn -query GCF_021398215.1_ASM2139821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153d75c5-b906-49a1-ad68-4aec91c18425/dqc_reference/reference_markers_gtdb.fasta -out GCF_021398215.1_ASM2139821v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:44,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:44,007] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:44,007] [INFO] Target genome list was writen to GCF_021398215.1_ASM2139821v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:44,050] [INFO] Task started: fastANI
[2024-01-24 13:41:44,050] [INFO] Running command: fastANI --query /var/lib/cwl/stga040d5d3-c630-44d2-a727-647d7968101e/GCF_021398215.1_ASM2139821v1_genomic.fna.gz --refList GCF_021398215.1_ASM2139821v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021398215.1_ASM2139821v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:56,870] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:56,886] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:41:56,887] [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_003185915.1	s__Specibacter psychrochitiniphilus	81.0221	627	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017353415.1	s__Specibacter sp017353415	80.9741	651	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785535.1	s__Specibacter sp000785535	80.4443	617	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001445575.1	s__Specibacter alpinus_C	80.2484	560	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909445.1	s__Specibacter glacialis	80.2313	592	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.29	99.29	0.92	0.92	2	-
GCF_017876675.1	s__Specibacter stackebrandtii	80.1201	587	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294625.1	s__Specibacter alpinus_A	80.1034	517	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.52	99.48	0.93	0.92	3	-
GCF_900105965.1	s__Specibacter alpinus	80.0637	551	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	96.92	96.92	0.91	0.91	2	-
GCF_002929705.1	s__Specibacter sp002929705	80.0452	571	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219795.1	s__Specibacter psychrolactophilus	79.9539	466	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281315.1	s__Specibacter sp001281315	79.857	498	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820535.1	s__Specibacter sp016820535	79.7819	557	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929305.1	s__Specibacter sp002929305	79.6195	490	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798705.1	s__Arthrobacter_I sp004798705	78.3612	211	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725815.1	s__Arthrobacter_I oryzae_A	77.9694	164	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,888] [INFO] GTDB search result was written to GCF_021398215.1_ASM2139821v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:56,889] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:56,893] [INFO] DFAST_QC result json was written to GCF_021398215.1_ASM2139821v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:56,893] [INFO] DFAST_QC completed!
[2024-01-24 13:41:56,893] [INFO] Total running time: 0h1m24s