[2024-01-24 14:14:44,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:44,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:44,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1eb8722-eb4b-47d9-bc56-da2119386bd5/dqc_reference
[2024-01-24 14:14:45,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:45,773] [INFO] Task started: Prodigal
[2024-01-24 14:14:45,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgde56d7d2-1d5b-4d00-b0ad-36f64e7108d4/GCF_012844445.1_ASM1284444v1_genomic.fna.gz | prodigal -d GCF_012844445.1_ASM1284444v1_genomic.fna/cds.fna -a GCF_012844445.1_ASM1284444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:52,261] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:52,262] [INFO] Task started: HMMsearch
[2024-01-24 14:14:52,263] [INFO] Running command: hmmsearch --tblout GCF_012844445.1_ASM1284444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1eb8722-eb4b-47d9-bc56-da2119386bd5/dqc_reference/reference_markers.hmm GCF_012844445.1_ASM1284444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:52,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:52,531] [INFO] Found 6/6 markers.
[2024-01-24 14:14:52,556] [INFO] Query marker FASTA was written to GCF_012844445.1_ASM1284444v1_genomic.fna/markers.fasta
[2024-01-24 14:14:52,557] [INFO] Task started: Blastn
[2024-01-24 14:14:52,557] [INFO] Running command: blastn -query GCF_012844445.1_ASM1284444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1eb8722-eb4b-47d9-bc56-da2119386bd5/dqc_reference/reference_markers.fasta -out GCF_012844445.1_ASM1284444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:53,253] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:53,257] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:53,258] [INFO] Target genome list was writen to GCF_012844445.1_ASM1284444v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:53,264] [INFO] Task started: fastANI
[2024-01-24 14:14:53,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgde56d7d2-1d5b-4d00-b0ad-36f64e7108d4/GCF_012844445.1_ASM1284444v1_genomic.fna.gz --refList GCF_012844445.1_ASM1284444v1_genomic.fna/target_genomes.txt --output GCF_012844445.1_ASM1284444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:00,221] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:00,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1eb8722-eb4b-47d9-bc56-da2119386bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:00,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1eb8722-eb4b-47d9-bc56-da2119386bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:00,266] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:00,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:00,267] [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 bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	95.5938	568	670	95	conclusive
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	81.3009	255	670	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	81.2901	255	670	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	81.21	256	670	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.4709	182	670	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.4604	183	670	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.4004	186	670	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.3811	210	670	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.1709	199	670	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	78.8412	179	670	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:00,293] [INFO] DFAST Taxonomy check result was written to GCF_012844445.1_ASM1284444v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:00,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:00,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:00,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1eb8722-eb4b-47d9-bc56-da2119386bd5/dqc_reference/checkm_data
[2024-01-24 14:15:00,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:00,325] [INFO] Task started: CheckM
[2024-01-24 14:15:00,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012844445.1_ASM1284444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012844445.1_ASM1284444v1_genomic.fna/checkm_input GCF_012844445.1_ASM1284444v1_genomic.fna/checkm_result
[2024-01-24 14:15:25,111] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:25,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:25,135] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:25,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:25,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012844445.1_ASM1284444v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:25,137] [INFO] Task started: Blastn
[2024-01-24 14:15:25,137] [INFO] Running command: blastn -query GCF_012844445.1_ASM1284444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1eb8722-eb4b-47d9-bc56-da2119386bd5/dqc_reference/reference_markers_gtdb.fasta -out GCF_012844445.1_ASM1284444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:26,463] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:26,467] [INFO] Selected 27 target genomes.
[2024-01-24 14:15:26,467] [INFO] Target genome list was writen to GCF_012844445.1_ASM1284444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:26,490] [INFO] Task started: fastANI
[2024-01-24 14:15:26,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgde56d7d2-1d5b-4d00-b0ad-36f64e7108d4/GCF_012844445.1_ASM1284444v1_genomic.fna.gz --refList GCF_012844445.1_ASM1284444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012844445.1_ASM1284444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:36,436] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:36,464] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:36,464] [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_900155365.1	s__Collinsella bouchesdurhonensis	95.5938	568	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.92	95.77	0.91	0.89	8	conclusive
GCF_901212495.1	s__Collinsella aerofaciens_H	81.3127	250	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.63	95.88	0.84	0.79	16	-
GCA_008671135.1	s__Collinsella aerofaciens_J	80.9174	241	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_900768435.1	s__Collinsella sp900768435	80.8766	237	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754275.1	s__Collinsella sp900754275	80.8308	224	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.49	95.11	0.84	0.77	3	-
GCA_900542635.1	s__Collinsella sp900542635	80.8286	229	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0787	N/A	N/A	N/A	N/A	1	-
GCA_900540985.1	s__Collinsella sp900540985	80.7473	231	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0011	97.54	95.11	0.88	0.81	3	-
GCA_900757265.1	s__Collinsella sp900757265	80.7168	140	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549455.1	s__Collinsella sp900549455	80.637	212	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.06	95.06	0.86	0.86	2	-
GCA_900547805.1	s__Collinsella sp900547805	80.5833	208	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548935.1	s__Collinsella sp900548935	80.5668	197	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015670745.1	s__Collinsella aerofaciens_T	80.5496	239	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0363	95.05	95.05	0.90	0.90	2	-
GCA_900551015.1	s__Collinsella sp900551015	80.5443	217	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.94	99.94	0.95	0.95	2	-
GCA_900551815.1	s__Collinsella sp900551815	80.5422	229	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549025.1	s__Collinsella sp900549025	80.5124	203	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0692	97.49	95.13	0.83	0.77	3	-
GCA_900543515.1	s__Collinsella sp900543515	80.4262	227	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1148	100.00	100.00	0.98	0.98	2	-
GCA_900756765.1	s__Collinsella sp900756765	80.3285	227	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542325.1	s__Collinsella sp900542325	80.2776	235	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900752345.1	s__Collinsella sp900752345	80.2547	176	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768795.1	s__Collinsella sp900768795	80.0933	205	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.75	98.75	0.86	0.86	2	-
GCF_900119895.1	s__Collinsella phocaeensis	79.3581	211	670	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	79.2837	209	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCF_016902615.1	s__Collinsella tanakaei_A	79.2808	194	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.95	98.95	0.92	0.92	2	-
GCF_000225705.1	s__Collinsella tanakaei	79.1601	200	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.30	95.17	0.91	0.86	6	-
GCA_019117005.1	s__Collinsella stercoripullorum	78.825	196	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCA_900540955.1	s__Paratractidigestivibacter sp900540955	78.8158	135	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.08	96.08	0.89	0.89	2	-
GCA_900548365.1	s__Collinsella sp900548365	78.7481	176	670	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:36,469] [INFO] GTDB search result was written to GCF_012844445.1_ASM1284444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:36,469] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:36,474] [INFO] DFAST_QC result json was written to GCF_012844445.1_ASM1284444v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:36,474] [INFO] DFAST_QC completed!
[2024-01-24 14:15:36,475] [INFO] Total running time: 0h0m52s