[2024-01-25 18:01:35,576] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:35,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:35,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg606d3dd1-a5b1-4326-bd70-52e99402665a/dqc_reference
[2024-01-25 18:01:36,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:36,743] [INFO] Task started: Prodigal
[2024-01-25 18:01:36,743] [INFO] Running command: gunzip -c /var/lib/cwl/stgc249c4a0-e28f-4683-bee1-da445624c361/GCF_016127995.1_ASM1612799v1_genomic.fna.gz | prodigal -d GCF_016127995.1_ASM1612799v1_genomic.fna/cds.fna -a GCF_016127995.1_ASM1612799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:42,331] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:42,331] [INFO] Task started: HMMsearch
[2024-01-25 18:01:42,331] [INFO] Running command: hmmsearch --tblout GCF_016127995.1_ASM1612799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg606d3dd1-a5b1-4326-bd70-52e99402665a/dqc_reference/reference_markers.hmm GCF_016127995.1_ASM1612799v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:42,508] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:42,511] [INFO] Found 6/6 markers.
[2024-01-25 18:01:42,541] [INFO] Query marker FASTA was written to GCF_016127995.1_ASM1612799v1_genomic.fna/markers.fasta
[2024-01-25 18:01:42,541] [INFO] Task started: Blastn
[2024-01-25 18:01:42,541] [INFO] Running command: blastn -query GCF_016127995.1_ASM1612799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606d3dd1-a5b1-4326-bd70-52e99402665a/dqc_reference/reference_markers.fasta -out GCF_016127995.1_ASM1612799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:43,456] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:43,459] [INFO] Selected 20 target genomes.
[2024-01-25 18:01:43,460] [INFO] Target genome list was writen to GCF_016127995.1_ASM1612799v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:43,471] [INFO] Task started: fastANI
[2024-01-25 18:01:43,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgc249c4a0-e28f-4683-bee1-da445624c361/GCF_016127995.1_ASM1612799v1_genomic.fna.gz --refList GCF_016127995.1_ASM1612799v1_genomic.fna/target_genomes.txt --output GCF_016127995.1_ASM1612799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:55,002] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:55,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg606d3dd1-a5b1-4326-bd70-52e99402665a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:55,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg606d3dd1-a5b1-4326-bd70-52e99402665a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:55,014] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:01:55,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:55,015] [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
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	100.0	677	677	95	conclusive
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	99.9858	654	677	95	conclusive
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	78.9278	203	677	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	78.4651	169	677	95	below_threshold
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	78.3281	116	677	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	78.3141	147	677	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	77.8924	102	677	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	77.8289	140	677	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	77.3864	105	677	95	below_threshold
Bowdeniella nasicola	strain=DSM 19116	GCA_001907295.1	208480	208480	type	True	77.3282	65	677	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	76.9377	62	677	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	76.9057	84	677	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	76.8451	88	677	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	76.5891	81	677	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	76.5444	80	677	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	76.492	82	677	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	76.4507	57	677	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	76.262	62	677	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	75.8469	55	677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:55,016] [INFO] DFAST Taxonomy check result was written to GCF_016127995.1_ASM1612799v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:55,016] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:55,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:55,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg606d3dd1-a5b1-4326-bd70-52e99402665a/dqc_reference/checkm_data
[2024-01-25 18:01:55,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:55,040] [INFO] Task started: CheckM
[2024-01-25 18:01:55,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127995.1_ASM1612799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127995.1_ASM1612799v1_genomic.fna/checkm_input GCF_016127995.1_ASM1612799v1_genomic.fna/checkm_result
[2024-01-25 18:02:15,372] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:15,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:15,388] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:15,388] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:15,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127995.1_ASM1612799v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:15,389] [INFO] Task started: Blastn
[2024-01-25 18:02:15,389] [INFO] Running command: blastn -query GCF_016127995.1_ASM1612799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606d3dd1-a5b1-4326-bd70-52e99402665a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127995.1_ASM1612799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:16,691] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:16,693] [INFO] Selected 13 target genomes.
[2024-01-25 18:02:16,694] [INFO] Target genome list was writen to GCF_016127995.1_ASM1612799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:16,696] [INFO] Task started: fastANI
[2024-01-25 18:02:16,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgc249c4a0-e28f-4683-bee1-da445624c361/GCF_016127995.1_ASM1612799v1_genomic.fna.gz --refList GCF_016127995.1_ASM1612799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127995.1_ASM1612799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:22,609] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:22,618] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:22,618] [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_900105015.1	s__Pauljensenia meyeri	99.9858	654	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	99.29	98.87	0.96	0.95	4	conclusive
GCF_000185285.1	s__Pauljensenia sp000185285	82.95	541	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.02	95.63	0.93	0.91	5	-
GCA_001072465.1	s__Pauljensenia sp001072465	82.6591	479	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_001838165.1	s__Pauljensenia sp001838165	82.639	479	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCA_018382595.1	s__Pauljensenia sp018382595	82.6235	429	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005696695.1	s__Pauljensenia odontolytica_C	82.6128	490	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCF_000466265.1	s__Pauljensenia sp000466265	82.5262	456	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.80	96.80	0.90	0.90	2	-
GCA_018375675.1	s__Pauljensenia sp018375675	82.4944	469	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001064145.1	s__Pauljensenia sp001064145	82.476	494	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	82.3668	498	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCF_000411415.1	s__Pauljensenia sp000411415	82.3633	491	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCA_902373545.1	s__Pauljensenia sp902373545	81.9359	414	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.43	97.43	0.84	0.84	2	-
GCA_900556405.1	s__Pauljensenia sp900556405	81.0481	320	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:22,620] [INFO] GTDB search result was written to GCF_016127995.1_ASM1612799v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:22,620] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:22,623] [INFO] DFAST_QC result json was written to GCF_016127995.1_ASM1612799v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:22,623] [INFO] DFAST_QC completed!
[2024-01-25 18:02:22,623] [INFO] Total running time: 0h0m47s