[2024-01-24 14:50:04,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:04,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:04,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg1489e643-7e06-40e0-866c-f67b35f6ee66/dqc_reference
[2024-01-24 14:50:05,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,744] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ed5c204-cb1d-4e73-9427-443fd0bb2b67/GCF_009646095.1_ASM964609v1_genomic.fna.gz | prodigal -d GCF_009646095.1_ASM964609v1_genomic.fna/cds.fna -a GCF_009646095.1_ASM964609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:17,176] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:17,176] [INFO] Task started: HMMsearch
[2024-01-24 14:50:17,176] [INFO] Running command: hmmsearch --tblout GCF_009646095.1_ASM964609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1489e643-7e06-40e0-866c-f67b35f6ee66/dqc_reference/reference_markers.hmm GCF_009646095.1_ASM964609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:17,449] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:17,450] [INFO] Found 6/6 markers.
[2024-01-24 14:50:17,487] [INFO] Query marker FASTA was written to GCF_009646095.1_ASM964609v1_genomic.fna/markers.fasta
[2024-01-24 14:50:17,487] [INFO] Task started: Blastn
[2024-01-24 14:50:17,487] [INFO] Running command: blastn -query GCF_009646095.1_ASM964609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1489e643-7e06-40e0-866c-f67b35f6ee66/dqc_reference/reference_markers.fasta -out GCF_009646095.1_ASM964609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:18,710] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:18,713] [INFO] Selected 20 target genomes.
[2024-01-24 14:50:18,713] [INFO] Target genome list was writen to GCF_009646095.1_ASM964609v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:18,719] [INFO] Task started: fastANI
[2024-01-24 14:50:18,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ed5c204-cb1d-4e73-9427-443fd0bb2b67/GCF_009646095.1_ASM964609v1_genomic.fna.gz --refList GCF_009646095.1_ASM964609v1_genomic.fna/target_genomes.txt --output GCF_009646095.1_ASM964609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:34,926] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:34,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1489e643-7e06-40e0-866c-f67b35f6ee66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:34,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1489e643-7e06-40e0-866c-f67b35f6ee66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:34,953] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:50:34,953] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:34,953] [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
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	100.0	1216	1216	95	conclusive
Raineyella antarctica	strain=LZ-22	GCA_900092135.1	1577474	1577474	type	True	81.9199	733	1216	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.8783	288	1216	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	77.8717	259	1216	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.8684	284	1216	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	77.8277	238	1216	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	77.8249	248	1216	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.8086	335	1216	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	77.7863	322	1216	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.7556	300	1216	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	77.7209	290	1216	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	77.6934	303	1216	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.4624	279	1216	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	77.3231	212	1216	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	77.1513	228	1216	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	76.7709	226	1216	95	below_threshold
Streptacidiphilus albus	strain=JL83	GCA_000744705.1	105425	105425	type	True	76.5381	289	1216	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	76.3359	278	1216	95	below_threshold
Streptomyces albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	76.1548	259	1216	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	76.1501	251	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:34,955] [INFO] DFAST Taxonomy check result was written to GCF_009646095.1_ASM964609v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:34,955] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:34,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:34,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1489e643-7e06-40e0-866c-f67b35f6ee66/dqc_reference/checkm_data
[2024-01-24 14:50:34,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:34,997] [INFO] Task started: CheckM
[2024-01-24 14:50:34,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009646095.1_ASM964609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009646095.1_ASM964609v1_genomic.fna/checkm_input GCF_009646095.1_ASM964609v1_genomic.fna/checkm_result
[2024-01-24 14:51:22,233] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:22,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:22,255] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:22,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:22,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009646095.1_ASM964609v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:22,256] [INFO] Task started: Blastn
[2024-01-24 14:51:22,256] [INFO] Running command: blastn -query GCF_009646095.1_ASM964609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1489e643-7e06-40e0-866c-f67b35f6ee66/dqc_reference/reference_markers_gtdb.fasta -out GCF_009646095.1_ASM964609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:23,953] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:23,957] [INFO] Selected 19 target genomes.
[2024-01-24 14:51:23,957] [INFO] Target genome list was writen to GCF_009646095.1_ASM964609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:23,966] [INFO] Task started: fastANI
[2024-01-24 14:51:23,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ed5c204-cb1d-4e73-9427-443fd0bb2b67/GCF_009646095.1_ASM964609v1_genomic.fna.gz --refList GCF_009646095.1_ASM964609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009646095.1_ASM964609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:39,544] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:39,561] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:39,562] [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_009646095.1	s__Raineyella sp009646095	100.0	1216	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900092135.1	s__Raineyella antarctica	81.9287	732	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.895	287	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_017569205.1	s__Brevilactibacter sp014164685	77.8268	296	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	99.00	98.00	0.92	0.83	3	-
GCF_004362375.1	s__Enemella evansiae	77.8177	291	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCF_015352975.1	s__Aestuariimicrobium ganziense	77.8126	249	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101785.1	s__Auraticoccus monumenti	77.812	321	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742705.1	s__Auraticoccus cholistanensis	77.7594	299	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838755.1	s__Brevilactibacter sp012838755	77.7419	256	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002250625.1	s__Enemella sp002250625	77.6993	292	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCF_016907175.1	s__Friedmanniella spumicola	77.6473	302	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	77.571	314	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105065.1	s__Friedmanniella luteola	77.4534	325	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	77.4528	286	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193425.1	s__Friedmanniella antarctica	77.4171	277	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517965.1	s__Propioniciclava sp012517965	77.4134	250	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	77.0025	207	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396125.1	s__Cellulomonas denverensis	76.7812	225	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000744705.1	s__Streptacidiphilus albus	76.471	291	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:39,563] [INFO] GTDB search result was written to GCF_009646095.1_ASM964609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:39,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:39,568] [INFO] DFAST_QC result json was written to GCF_009646095.1_ASM964609v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:39,568] [INFO] DFAST_QC completed!
[2024-01-24 14:51:39,568] [INFO] Total running time: 0h1m35s