[2024-01-24 11:43:25,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg312a3a38-2d4a-4609-b895-ac100ec86d9b/dqc_reference
[2024-01-24 11:43:30,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,063] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c9da0af-3dbb-45b8-a84f-69189bb0d523/GCF_002563675.1_ASM256367v1_genomic.fna.gz | prodigal -d GCF_002563675.1_ASM256367v1_genomic.fna/cds.fna -a GCF_002563675.1_ASM256367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:40,058] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:40,059] [INFO] Task started: HMMsearch
[2024-01-24 11:43:40,059] [INFO] Running command: hmmsearch --tblout GCF_002563675.1_ASM256367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg312a3a38-2d4a-4609-b895-ac100ec86d9b/dqc_reference/reference_markers.hmm GCF_002563675.1_ASM256367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:40,353] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:40,354] [INFO] Found 6/6 markers.
[2024-01-24 11:43:40,386] [INFO] Query marker FASTA was written to GCF_002563675.1_ASM256367v1_genomic.fna/markers.fasta
[2024-01-24 11:43:40,386] [INFO] Task started: Blastn
[2024-01-24 11:43:40,386] [INFO] Running command: blastn -query GCF_002563675.1_ASM256367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg312a3a38-2d4a-4609-b895-ac100ec86d9b/dqc_reference/reference_markers.fasta -out GCF_002563675.1_ASM256367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:41,521] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:41,526] [INFO] Selected 19 target genomes.
[2024-01-24 11:43:41,527] [INFO] Target genome list was writen to GCF_002563675.1_ASM256367v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:41,535] [INFO] Task started: fastANI
[2024-01-24 11:43:41,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c9da0af-3dbb-45b8-a84f-69189bb0d523/GCF_002563675.1_ASM256367v1_genomic.fna.gz --refList GCF_002563675.1_ASM256367v1_genomic.fna/target_genomes.txt --output GCF_002563675.1_ASM256367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:56,043] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:56,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg312a3a38-2d4a-4609-b895-ac100ec86d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:56,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg312a3a38-2d4a-4609-b895-ac100ec86d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:56,059] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:56,060] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:56,060] [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
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	100.0	1084	1087	95	conclusive
Micropruina glycogenica		GCA_900289045.1	75385	75385	type	True	78.5708	325	1087	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.4789	314	1087	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.4048	258	1087	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.3343	261	1087	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	78.2601	306	1087	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.1625	267	1087	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	78.1487	268	1087	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	78.0122	309	1087	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	77.8388	291	1087	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.7465	234	1087	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	77.7189	288	1087	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	77.7087	260	1087	95	below_threshold
Microlunatus endophyticus	strain=CGMCC 4.7306	GCA_014646195.1	1716077	1716077	type	True	77.7003	211	1087	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.6471	243	1087	95	below_threshold
Propionicicella superfundia	strain=DSM 22317	GCA_000423465.1	348582	348582	type	True	77.6392	226	1087	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.0689	241	1087	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	76.3142	232	1087	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	76.1433	223	1087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:56,063] [INFO] DFAST Taxonomy check result was written to GCF_002563675.1_ASM256367v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:56,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:56,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:56,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg312a3a38-2d4a-4609-b895-ac100ec86d9b/dqc_reference/checkm_data
[2024-01-24 11:43:56,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:56,101] [INFO] Task started: CheckM
[2024-01-24 11:43:56,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563675.1_ASM256367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563675.1_ASM256367v1_genomic.fna/checkm_input GCF_002563675.1_ASM256367v1_genomic.fna/checkm_result
[2024-01-24 11:44:30,798] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:30,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:30,819] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:30,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:30,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563675.1_ASM256367v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:30,821] [INFO] Task started: Blastn
[2024-01-24 11:44:30,821] [INFO] Running command: blastn -query GCF_002563675.1_ASM256367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg312a3a38-2d4a-4609-b895-ac100ec86d9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563675.1_ASM256367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:32,466] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:32,470] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:32,470] [INFO] Target genome list was writen to GCF_002563675.1_ASM256367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:32,477] [INFO] Task started: fastANI
[2024-01-24 11:44:32,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c9da0af-3dbb-45b8-a84f-69189bb0d523/GCF_002563675.1_ASM256367v1_genomic.fna.gz --refList GCF_002563675.1_ASM256367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563675.1_ASM256367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:39,452] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:39,465] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:39,466] [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_002563675.1	s__Propionicimonas paludicola	100.0	1085	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001603275.1	s__Propionicimonas sp001603275	87.0333	827	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	80.312	500	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841335.1	s__Propionicimonas sp002841335	80.2877	499	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441465.1	s__Propionicimonas sp002441465	80.2395	324	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306015.1	s__Propionicimonas sp017306015	80.2014	536	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882685.1	s__Propionicimonas sp017882685	79.4804	399	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693855.1	s__Micropruina sp013693855	79.2015	357	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	78.4591	332	1087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:39,468] [INFO] GTDB search result was written to GCF_002563675.1_ASM256367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:39,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:39,474] [INFO] DFAST_QC result json was written to GCF_002563675.1_ASM256367v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:39,475] [INFO] DFAST_QC completed!
[2024-01-24 11:44:39,475] [INFO] Total running time: 0h1m14s