[2023-06-29 01:46:23,315] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:46:23,319] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:46:23,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg63553fa2-aaee-4ae4-9d86-668a1bc1e4c6/dqc_reference
[2023-06-29 01:46:24,712] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:46:24,714] [INFO] Task started: Prodigal
[2023-06-29 01:46:24,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg13b71c2a-66da-4beb-86ea-9fd96c950a99/GCA_015062655.1_ASM1506265v1_genomic.fna.gz | prodigal -d GCA_015062655.1_ASM1506265v1_genomic.fna/cds.fna -a GCA_015062655.1_ASM1506265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:46:30,857] [INFO] Task succeeded: Prodigal
[2023-06-29 01:46:30,857] [INFO] Task started: HMMsearch
[2023-06-29 01:46:30,857] [INFO] Running command: hmmsearch --tblout GCA_015062655.1_ASM1506265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63553fa2-aaee-4ae4-9d86-668a1bc1e4c6/dqc_reference/reference_markers.hmm GCA_015062655.1_ASM1506265v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:46:31,074] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:46:31,076] [INFO] Found 6/6 markers.
[2023-06-29 01:46:31,122] [INFO] Query marker FASTA was written to GCA_015062655.1_ASM1506265v1_genomic.fna/markers.fasta
[2023-06-29 01:46:31,123] [INFO] Task started: Blastn
[2023-06-29 01:46:31,123] [INFO] Running command: blastn -query GCA_015062655.1_ASM1506265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63553fa2-aaee-4ae4-9d86-668a1bc1e4c6/dqc_reference/reference_markers.fasta -out GCA_015062655.1_ASM1506265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:46:31,937] [INFO] Task succeeded: Blastn
[2023-06-29 01:46:31,942] [INFO] Selected 13 target genomes.
[2023-06-29 01:46:31,942] [INFO] Target genome list was writen to GCA_015062655.1_ASM1506265v1_genomic.fna/target_genomes.txt
[2023-06-29 01:46:31,973] [INFO] Task started: fastANI
[2023-06-29 01:46:31,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b71c2a-66da-4beb-86ea-9fd96c950a99/GCA_015062655.1_ASM1506265v1_genomic.fna.gz --refList GCA_015062655.1_ASM1506265v1_genomic.fna/target_genomes.txt --output GCA_015062655.1_ASM1506265v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:46:38,586] [INFO] Task succeeded: fastANI
[2023-06-29 01:46:38,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63553fa2-aaee-4ae4-9d86-668a1bc1e4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:46:38,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63553fa2-aaee-4ae4-9d86-668a1bc1e4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:46:38,599] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:46:38,599] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 01:46:38,599] [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
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	83.6419	425	677	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	80.8018	322	677	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	80.7615	278	677	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.4112	283	677	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	80.1511	249	677	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.0979	309	677	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.0079	314	677	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	79.2282	227	677	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.2189	246	677	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.0596	214	677	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.7101	186	677	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.5749	208	677	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	75.0558	95	677	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 01:46:38,603] [INFO] DFAST Taxonomy check result was written to GCA_015062655.1_ASM1506265v1_genomic.fna/tc_result.tsv
[2023-06-29 01:46:38,604] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:46:38,605] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:46:38,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63553fa2-aaee-4ae4-9d86-668a1bc1e4c6/dqc_reference/checkm_data
[2023-06-29 01:46:38,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:46:38,647] [INFO] Task started: CheckM
[2023-06-29 01:46:38,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015062655.1_ASM1506265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015062655.1_ASM1506265v1_genomic.fna/checkm_input GCA_015062655.1_ASM1506265v1_genomic.fna/checkm_result
[2023-06-29 01:47:01,894] [INFO] Task succeeded: CheckM
[2023-06-29 01:47:01,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:47:01,917] [INFO] ===== Completeness check finished =====
[2023-06-29 01:47:01,917] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:47:01,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015062655.1_ASM1506265v1_genomic.fna/markers.fasta)
[2023-06-29 01:47:01,918] [INFO] Task started: Blastn
[2023-06-29 01:47:01,918] [INFO] Running command: blastn -query GCA_015062655.1_ASM1506265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63553fa2-aaee-4ae4-9d86-668a1bc1e4c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_015062655.1_ASM1506265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:47:03,502] [INFO] Task succeeded: Blastn
[2023-06-29 01:47:03,507] [INFO] Selected 16 target genomes.
[2023-06-29 01:47:03,508] [INFO] Target genome list was writen to GCA_015062655.1_ASM1506265v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:47:03,520] [INFO] Task started: fastANI
[2023-06-29 01:47:03,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b71c2a-66da-4beb-86ea-9fd96c950a99/GCA_015062655.1_ASM1506265v1_genomic.fna.gz --refList GCA_015062655.1_ASM1506265v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015062655.1_ASM1506265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:47:10,467] [INFO] Task succeeded: fastANI
[2023-06-29 01:47:10,481] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 01:47:10,481] [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
GCA_015062655.1	s__Collinsella sp015062655	100.0	674	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176655.1	s__Collinsella vaginalis	83.6202	426	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.31	99.31	0.99	0.99	2	-
GCF_902501965.1	s__Collinsella sp900556495	81.1576	321	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.47	98.05	0.92	0.92	3	-
GCA_019117005.1	s__Collinsella stercoripullorum	80.9847	306	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_902150035.1	s__Enorma burkinafasonensis	80.8614	319	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333815.1	s__Enorma sp000333815	80.682	275	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCF_016902615.1	s__Collinsella tanakaei_A	80.4651	299	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.95	98.95	0.92	0.92	2	-
GCF_900119895.1	s__Collinsella phocaeensis	80.4113	283	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCF_016900375.1	s__Collinsella sp002305035	80.386	303	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCA_900551665.1	s__Collinsella sp900551665	80.0412	200	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156215.1	s__Collinsella stercoris	79.9973	315	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.61	95.23	0.87	0.81	5	-
GCF_014982725.1	s__Thermophilibacter sp014982725	79.3792	208	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159625.1	s__Thermophilibacter avicola	79.2697	194	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCA_900555585.1	s__Collinsella sp900555585	79.1991	123	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900543875.1	s__Parolsenella sp900543875	78.5065	191	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.15	98.15	0.88	0.88	2	-
GCA_015062635.1	s__UMGS1519 sp015062635	76.7455	78	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UMGS1519	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 01:47:10,483] [INFO] GTDB search result was written to GCA_015062655.1_ASM1506265v1_genomic.fna/result_gtdb.tsv
[2023-06-29 01:47:10,484] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:47:10,488] [INFO] DFAST_QC result json was written to GCA_015062655.1_ASM1506265v1_genomic.fna/dqc_result.json
[2023-06-29 01:47:10,488] [INFO] DFAST_QC completed!
[2023-06-29 01:47:10,488] [INFO] Total running time: 0h0m47s