[2024-01-25 18:00:50,729] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:50,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:50,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgad7e4a06-0b90-486b-a9a0-194176b05fb9/dqc_reference
[2024-01-25 18:00:51,848] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:51,848] [INFO] Task started: Prodigal
[2024-01-25 18:00:51,849] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6b57929-4869-4843-8d2d-7fb40683056b/GCF_014926385.1_ASM1492638v1_genomic.fna.gz | prodigal -d GCF_014926385.1_ASM1492638v1_genomic.fna/cds.fna -a GCF_014926385.1_ASM1492638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:58,056] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:58,056] [INFO] Task started: HMMsearch
[2024-01-25 18:00:58,056] [INFO] Running command: hmmsearch --tblout GCF_014926385.1_ASM1492638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad7e4a06-0b90-486b-a9a0-194176b05fb9/dqc_reference/reference_markers.hmm GCF_014926385.1_ASM1492638v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:58,242] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:58,243] [INFO] Found 6/6 markers.
[2024-01-25 18:00:58,264] [INFO] Query marker FASTA was written to GCF_014926385.1_ASM1492638v1_genomic.fna/markers.fasta
[2024-01-25 18:00:58,264] [INFO] Task started: Blastn
[2024-01-25 18:00:58,264] [INFO] Running command: blastn -query GCF_014926385.1_ASM1492638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad7e4a06-0b90-486b-a9a0-194176b05fb9/dqc_reference/reference_markers.fasta -out GCF_014926385.1_ASM1492638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:59,068] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:59,071] [INFO] Selected 20 target genomes.
[2024-01-25 18:00:59,072] [INFO] Target genome list was writen to GCF_014926385.1_ASM1492638v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:59,090] [INFO] Task started: fastANI
[2024-01-25 18:00:59,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b57929-4869-4843-8d2d-7fb40683056b/GCF_014926385.1_ASM1492638v1_genomic.fna.gz --refList GCF_014926385.1_ASM1492638v1_genomic.fna/target_genomes.txt --output GCF_014926385.1_ASM1492638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:12,415] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:12,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad7e4a06-0b90-486b-a9a0-194176b05fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:12,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad7e4a06-0b90-486b-a9a0-194176b05fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:12,424] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:12,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:12,425] [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
Trueperella pecoris	strain=19M2397	GCA_014926385.1	2733571	2733571	type	True	100.0	759	760	95	conclusive
Trueperella pyogenes	strain=NCTC5224	GCA_900460345.1	1661	1661	type	True	80.9437	370	760	95	below_threshold
Trueperella pyogenes	strain=DSM 20630	GCA_014191445.1	1661	1661	type	True	80.8428	345	760	95	below_threshold
Trueperella bernardiae	strain=LCDC 89-0504	GCA_001469025.1	59561	59561	type	True	79.6598	355	760	95	below_threshold
Trueperella bialowiezensis	strain=NCTC13354	GCA_900637955.1	312285	312285	type	True	77.9905	173	760	95	below_threshold
Flaviflexus salsibiostraticola	strain=KCTC 33148	GCA_003952265.1	1282737	1282737	type	True	77.635	103	760	95	below_threshold
Flaviflexus equikiangi	strain=dk850	GCA_014069875.1	2758573	2758573	type	True	77.5685	79	760	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	77.172	75	760	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	76.3197	70	760	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	76.3062	64	760	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.2021	66	760	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	76.1443	62	760	95	below_threshold
Brachybacterium subflavum	strain=CFH 10395	GCA_009299795.1	2585206	2585206	type	True	76.0111	60	760	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	75.5477	60	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:12,426] [INFO] DFAST Taxonomy check result was written to GCF_014926385.1_ASM1492638v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:12,426] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:12,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:12,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad7e4a06-0b90-486b-a9a0-194176b05fb9/dqc_reference/checkm_data
[2024-01-25 18:01:12,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:12,453] [INFO] Task started: CheckM
[2024-01-25 18:01:12,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014926385.1_ASM1492638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014926385.1_ASM1492638v1_genomic.fna/checkm_input GCF_014926385.1_ASM1492638v1_genomic.fna/checkm_result
[2024-01-25 18:01:34,861] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:34,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:34,895] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:34,895] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:34,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014926385.1_ASM1492638v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:34,896] [INFO] Task started: Blastn
[2024-01-25 18:01:34,896] [INFO] Running command: blastn -query GCF_014926385.1_ASM1492638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad7e4a06-0b90-486b-a9a0-194176b05fb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014926385.1_ASM1492638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:36,094] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:36,097] [INFO] Selected 19 target genomes.
[2024-01-25 18:01:36,097] [INFO] Target genome list was writen to GCF_014926385.1_ASM1492638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:36,115] [INFO] Task started: fastANI
[2024-01-25 18:01:36,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b57929-4869-4843-8d2d-7fb40683056b/GCF_014926385.1_ASM1492638v1_genomic.fna.gz --refList GCF_014926385.1_ASM1492638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014926385.1_ASM1492638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:48,640] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:48,651] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:48,651] [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_014926385.1	s__Trueperella pecoris	100.0	758	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	97.88	95.38	0.92	0.88	4	conclusive
GCF_900460345.1	s__Trueperella pyogenes	80.8974	369	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	98.61	97.91	0.94	0.87	20	-
GCF_001469025.1	s__Trueperella bernardiae	79.6562	356	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	99.54	99.43	0.95	0.94	5	-
GCF_900637955.1	s__Trueperella bialowiezensis	77.9144	173	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952265.1	s__Flaviflexus salsibiostraticola	77.5108	103	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012727825.1	s__Trueperella sp012727825	77.2266	97	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	77.0155	59	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054555.1	s__Streptomyces lunaelactis	76.696	50	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.21	97.91	0.90	0.85	18	-
GCF_002798015.1	s__Luteimicrobium subarcticum	76.6362	69	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696205.1	s__Cellulomonas sp003696205	76.4174	71	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149805.1	s__Isoptericola chiayiensis	76.3371	63	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623465.1	s__Brachybacterium halotolerans	76.3197	70	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	76.316	67	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096585.1	s__Sanguibacter gelidistatuariae	76.1443	62	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	76.0708	69	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_009299795.1	s__Brachybacterium subflavum	76.0111	60	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773415.1	s__RUG11864 sp902773415	75.9818	56	760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__RUG11864	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:48,654] [INFO] GTDB search result was written to GCF_014926385.1_ASM1492638v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:48,654] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:48,668] [INFO] DFAST_QC result json was written to GCF_014926385.1_ASM1492638v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:48,668] [INFO] DFAST_QC completed!
[2024-01-25 18:01:48,668] [INFO] Total running time: 0h0m58s